diff --git a/backend/app/gateway/routers/thread_runs.py b/backend/app/gateway/routers/thread_runs.py
index c3e2ee7b9..1410e8964 100644
--- a/backend/app/gateway/routers/thread_runs.py
+++ b/backend/app/gateway/routers/thread_runs.py
@@ -79,7 +79,10 @@ class RunResponse(BaseModel):
 
 class ThreadTokenUsageModelBreakdown(BaseModel):
     tokens: int = 0
-    runs: int = 0
+    runs: int = Field(
+        default=0,
+        description="Number of runs in which this model appeared; counts are non-exclusive for runs that used multiple models.",
+    )
 
 
 class ThreadTokenUsageCallerBreakdown(BaseModel):
diff --git a/backend/packages/harness/deerflow/persistence/run/model.py b/backend/packages/harness/deerflow/persistence/run/model.py
index d0dfe4085..4fa7fc3ad 100644
--- a/backend/packages/harness/deerflow/persistence/run/model.py
+++ b/backend/packages/harness/deerflow/persistence/run/model.py
@@ -39,6 +39,8 @@ class RunRow(Base):
     lead_agent_tokens: Mapped[int] = mapped_column(default=0)
     subagent_tokens: Mapped[int] = mapped_column(default=0)
     middleware_tokens: Mapped[int] = mapped_column(default=0)
+    # Per-model token breakdown
+    token_usage_by_model: Mapped[dict] = mapped_column(JSON, default=dict)
 
     # Follow-up association
     follow_up_to_run_id: Mapped[str | None] = mapped_column(String(64))
diff --git a/backend/packages/harness/deerflow/persistence/run/sql.py b/backend/packages/harness/deerflow/persistence/run/sql.py
index 7ca2ea1e1..91968c04d 100644
--- a/backend/packages/harness/deerflow/persistence/run/sql.py
+++ b/backend/packages/harness/deerflow/persistence/run/sql.py
@@ -11,7 +11,7 @@ import json
 from datetime import UTC, datetime
 from typing import Any
 
-from sqlalchemy import func, select, update
+from sqlalchemy import select, update
 from sqlalchemy.ext.asyncio import AsyncSession, async_sessionmaker
 
 from deerflow.persistence.run.model import RunRow
@@ -230,6 +230,7 @@ class RunRepository(RunStore):
         lead_agent_tokens: int = 0,
         subagent_tokens: int = 0,
         middleware_tokens: int = 0,
+        token_usage_by_model: dict[str, dict[str, int]] | None = None,
         message_count: int = 0,
         last_ai_message: str | None = None,
         first_human_message: str | None = None,
@@ -248,6 +249,7 @@ class RunRepository(RunStore):
             "lead_agent_tokens": lead_agent_tokens,
             "subagent_tokens": subagent_tokens,
             "middleware_tokens": middleware_tokens,
+            "token_usage_by_model": self._safe_json(token_usage_by_model) or {},
             "message_count": message_count,
             "updated_at": datetime.now(UTC),
         }
@@ -273,6 +275,7 @@ class RunRepository(RunStore):
         lead_agent_tokens: int | None = None,
         subagent_tokens: int | None = None,
         middleware_tokens: int | None = None,
+        token_usage_by_model: dict[str, dict[str, int]] | None = None,
         message_count: int | None = None,
         last_ai_message: str | None = None,
         first_human_message: str | None = None,
@@ -292,6 +295,8 @@ class RunRepository(RunStore):
         for key, value in optional_counters.items():
             if value is not None:
                 values[key] = value
+        if token_usage_by_model is not None:
+            values["token_usage_by_model"] = self._safe_json(token_usage_by_model) or {}
         if last_ai_message is not None:
             values["last_ai_message"] = last_ai_message[:2000]
         if first_human_message is not None:
@@ -301,26 +306,33 @@ class RunRepository(RunStore):
             await session.commit()
 
     async def aggregate_tokens_by_thread(self, thread_id: str, *, include_active: bool = False) -> dict[str, Any]:
-        """Aggregate token usage via a single SQL GROUP BY query."""
+        """Aggregate token usage for a thread.
+
+        ``by_model`` is reduced in Python from each row's ``token_usage_by_model``
+        JSON column so subagent / middleware tokens land on the model that
+        actually produced them (issue #3645). Rows written before that column
+        existed fall back to ``RunRow.model_name`` + ``RunRow.total_tokens``,
+        preserving the legacy lead-only behavior instead of dropping the data.
+
+        Headline totals (``total_tokens``, ``total_input_tokens``,
+        ``total_output_tokens``) and the ``by_caller`` bucket are summed from
+        their own columns and are therefore unaffected by the JSON column being
+        empty.
+        """
         statuses = ("success", "error", "running") if include_active else ("success", "error")
         _completed = RunRow.status.in_(statuses)
         _thread = RunRow.thread_id == thread_id
-        model_name = func.coalesce(RunRow.model_name, "unknown")
 
-        stmt = (
-            select(
-                model_name.label("model"),
-                func.count().label("runs"),
-                func.coalesce(func.sum(RunRow.total_tokens), 0).label("total_tokens"),
-                func.coalesce(func.sum(RunRow.total_input_tokens), 0).label("total_input_tokens"),
-                func.coalesce(func.sum(RunRow.total_output_tokens), 0).label("total_output_tokens"),
-                func.coalesce(func.sum(RunRow.lead_agent_tokens), 0).label("lead_agent"),
-                func.coalesce(func.sum(RunRow.subagent_tokens), 0).label("subagent"),
-                func.coalesce(func.sum(RunRow.middleware_tokens), 0).label("middleware"),
-            )
-            .where(_thread, _completed)
-            .group_by(model_name)
-        )
+        stmt = select(
+            RunRow.model_name,
+            RunRow.total_tokens,
+            RunRow.total_input_tokens,
+            RunRow.total_output_tokens,
+            RunRow.lead_agent_tokens,
+            RunRow.subagent_tokens,
+            RunRow.middleware_tokens,
+            RunRow.token_usage_by_model,
+        ).where(_thread, _completed)
 
         async with self._sf() as session:
             rows = (await session.execute(stmt)).all()
@@ -329,14 +341,28 @@ class RunRepository(RunStore):
         lead_agent = subagent = middleware = 0
         by_model: dict[str, dict] = {}
         for r in rows:
-            by_model[r.model] = {"tokens": r.total_tokens, "runs": r.runs}
+            total_runs += 1
             total_tokens += r.total_tokens
             total_input += r.total_input_tokens
             total_output += r.total_output_tokens
-            total_runs += r.runs
-            lead_agent += r.lead_agent
-            subagent += r.subagent
-            middleware += r.middleware
+            lead_agent += r.lead_agent_tokens
+            subagent += r.subagent_tokens
+            middleware += r.middleware_tokens
+
+            # ``or {}`` covers rows written before ``token_usage_by_model``
+            # existed (the column is NULL on a manual ALTER ADD COLUMN without
+            # backfill); fresh rows always carry the journal-produced dict.
+            usage_by_model = r.token_usage_by_model or {}
+            if usage_by_model:
+                for model, usage in usage_by_model.items():
+                    entry = by_model.setdefault(model, {"tokens": 0, "runs": 0})
+                    entry["tokens"] += usage.get("total_tokens", 0)
+                    entry["runs"] += 1
+            else:
+                model = r.model_name or "unknown"
+                entry = by_model.setdefault(model, {"tokens": 0, "runs": 0})
+                entry["tokens"] += r.total_tokens
+                entry["runs"] += 1
 
         return {
             "total_tokens": total_tokens,
diff --git a/backend/packages/harness/deerflow/runtime/journal.py b/backend/packages/harness/deerflow/runtime/journal.py
index 74e03f165..ffbd7479f 100644
--- a/backend/packages/harness/deerflow/runtime/journal.py
+++ b/backend/packages/harness/deerflow/runtime/journal.py
@@ -77,6 +77,9 @@ class RunJournal(BaseCallbackHandler):
         self._subagent_tokens = 0
         self._middleware_tokens = 0
 
+        # Per-model token accumulator
+        self._tokens_by_model: dict[str, dict[str, int]] = {}
+
         # Dedup: LangChain may fire on_llm_end multiple times for the same run_id
         self._counted_llm_run_ids: set[str] = set()
         self._counted_external_source_ids: set[str] = set()
@@ -327,6 +330,13 @@ class RunJournal(BaseCallbackHandler):
                     else:
                         self._lead_agent_tokens += total_tk
 
+                    # Per-model bucket
+                    response_metadata = getattr(message, "response_metadata", None) or {}
+                    per_call_model: str | None = None
+                    if isinstance(response_metadata, Mapping):
+                        per_call_model = response_metadata.get("model_name") or response_metadata.get("model")
+                    self._record_model_usage(per_call_model, input_tk, output_tk, total_tk)
+
                     self._schedule_progress_flush()
 
         if messages:
@@ -435,17 +445,42 @@ class RunJournal(BaseCallbackHandler):
         # themselves.
         return "lead_agent"
 
+    def _record_model_usage(
+        self,
+        model_name: str | None,
+        input_tokens: int,
+        output_tokens: int,
+        total_tokens: int,
+    ) -> None:
+        """Add a single LLM call's token usage to the per-model accumulator.
+
+        Missing / empty ``model_name`` collapses into a shared ``"unknown"``
+        bucket so the breakdown stays usable when a provider doesn't surface
+        ``response_metadata.model_name``.
+        """
+        if total_tokens <= 0:
+            return
+        bucket = self._tokens_by_model.setdefault(
+            model_name or "unknown",
+            {"input_tokens": 0, "output_tokens": 0, "total_tokens": 0},
+        )
+        bucket["input_tokens"] += int(input_tokens or 0)
+        bucket["output_tokens"] += int(output_tokens or 0)
+        bucket["total_tokens"] += int(total_tokens)
+
     # -- Public methods (called by worker) --
 
     def record_external_llm_usage_records(
         self,
-        records: list[dict[str, int | str]],
+        records: list[dict[str, int | str | None]],
     ) -> None:
         """Record token usage from external sources (e.g., subagents).
 
         Each record should contain:
             source_run_id: Unique identifier to prevent double-counting
             caller: Caller tag (e.g. "subagent:general-purpose")
+            model_name: Real per-call model name (str or None; falls back to
+                ``"unknown"`` bucket when missing)
             input_tokens: Input token count
             output_tokens: Output token count
             total_tokens: Total token count (computed from input+output if 0/missing)
@@ -467,9 +502,12 @@ class RunJournal(BaseCallbackHandler):
             if total_tk <= 0:
                 continue
 
+            input_tk = record.get("input_tokens", 0) or 0
+            output_tk = record.get("output_tokens", 0) or 0
+
             self._counted_external_source_ids.add(source_id)
-            self._total_input_tokens += record.get("input_tokens", 0) or 0
-            self._total_output_tokens += record.get("output_tokens", 0) or 0
+            self._total_input_tokens += input_tk
+            self._total_output_tokens += output_tk
             self._total_tokens += total_tk
 
             caller = str(record.get("caller", ""))
@@ -480,6 +518,8 @@ class RunJournal(BaseCallbackHandler):
             else:
                 self._lead_agent_tokens += total_tk
 
+            self._record_model_usage(record.get("model_name"), input_tk, output_tk, total_tk)
+
             self._schedule_progress_flush()
 
     def set_first_human_message(self, content: str) -> None:
@@ -590,6 +630,7 @@ class RunJournal(BaseCallbackHandler):
             "lead_agent_tokens": self._lead_agent_tokens,
             "subagent_tokens": self._subagent_tokens,
             "middleware_tokens": self._middleware_tokens,
+            "token_usage_by_model": {model: dict(usage) for model, usage in self._tokens_by_model.items()},
             "message_count": self._msg_count,
             "last_ai_message": self._last_ai_msg,
             "first_human_message": self._first_human_msg,
diff --git a/backend/packages/harness/deerflow/runtime/runs/manager.py b/backend/packages/harness/deerflow/runtime/runs/manager.py
index a1e93c68c..4b52d0aca 100644
--- a/backend/packages/harness/deerflow/runtime/runs/manager.py
+++ b/backend/packages/harness/deerflow/runtime/runs/manager.py
@@ -99,6 +99,8 @@ class RunRecord:
     lead_agent_tokens: int = 0
     subagent_tokens: int = 0
     middleware_tokens: int = 0
+    # Per-model token breakdown
+    token_usage_by_model: dict[str, dict[str, int]] = field(default_factory=dict)
     message_count: int = 0
     last_ai_message: str | None = None
     first_human_message: str | None = None
@@ -291,6 +293,7 @@ class RunManager:
             lead_agent_tokens=row.get("lead_agent_tokens") or 0,
             subagent_tokens=row.get("subagent_tokens") or 0,
             middleware_tokens=row.get("middleware_tokens") or 0,
+            token_usage_by_model=row.get("token_usage_by_model") or {},
             message_count=row.get("message_count") or 0,
             last_ai_message=row.get("last_ai_message"),
             first_human_message=row.get("first_human_message"),
diff --git a/backend/packages/harness/deerflow/runtime/runs/store/base.py b/backend/packages/harness/deerflow/runtime/runs/store/base.py
index 071f1436f..682adeaea 100644
--- a/backend/packages/harness/deerflow/runtime/runs/store/base.py
+++ b/backend/packages/harness/deerflow/runtime/runs/store/base.py
@@ -93,6 +93,7 @@ class RunStore(abc.ABC):
         lead_agent_tokens: int = 0,
         subagent_tokens: int = 0,
         middleware_tokens: int = 0,
+        token_usage_by_model: dict[str, dict[str, int]] | None = None,
         message_count: int = 0,
         last_ai_message: str | None = None,
         first_human_message: str | None = None,
@@ -115,6 +116,7 @@ class RunStore(abc.ABC):
         lead_agent_tokens: int | None = None,
         subagent_tokens: int | None = None,
         middleware_tokens: int | None = None,
+        token_usage_by_model: dict[str, dict[str, int]] | None = None,
         message_count: int | None = None,
         last_ai_message: str | None = None,
         first_human_message: str | None = None,
diff --git a/backend/packages/harness/deerflow/runtime/runs/store/memory.py b/backend/packages/harness/deerflow/runtime/runs/store/memory.py
index 743240723..0cb4e82cc 100644
--- a/backend/packages/harness/deerflow/runtime/runs/store/memory.py
+++ b/backend/packages/harness/deerflow/runtime/runs/store/memory.py
@@ -110,10 +110,21 @@ class MemoryRunStore(RunStore):
         completed = [r for r in self._runs.values() if r["thread_id"] == thread_id and r.get("status") in statuses]
         by_model: dict[str, dict] = {}
         for r in completed:
-            model = r.get("model_name") or "unknown"
-            entry = by_model.setdefault(model, {"tokens": 0, "runs": 0})
-            entry["tokens"] += r.get("total_tokens", 0)
-            entry["runs"] += 1
+            usage_by_model = r.get("token_usage_by_model") or {}
+            if usage_by_model:
+                for model, usage in usage_by_model.items():
+                    entry = by_model.setdefault(model, {"tokens": 0, "runs": 0})
+                    entry["tokens"] += usage.get("total_tokens", 0)
+                    entry["runs"] += 1
+            else:
+                # Fallback for rows written before per-model accounting landed:
+                # attribute the whole run to its single ``model_name``. Keeps
+                # the legacy lead-only behavior for old data instead of
+                # silently dropping it.
+                model = r.get("model_name") or "unknown"
+                entry = by_model.setdefault(model, {"tokens": 0, "runs": 0})
+                entry["tokens"] += r.get("total_tokens", 0)
+                entry["runs"] += 1
         return {
             "total_tokens": sum(r.get("total_tokens", 0) for r in completed),
             "total_input_tokens": sum(r.get("total_input_tokens", 0) for r in completed),
diff --git a/backend/packages/harness/deerflow/subagents/executor.py b/backend/packages/harness/deerflow/subagents/executor.py
index 16c123d78..a89df4066 100644
--- a/backend/packages/harness/deerflow/subagents/executor.py
+++ b/backend/packages/harness/deerflow/subagents/executor.py
@@ -89,7 +89,7 @@ class SubagentResult:
     started_at: datetime | None = None
     completed_at: datetime | None = None
     ai_messages: list[dict[str, Any]] | None = None
-    token_usage_records: list[dict[str, int | str]] = field(default_factory=list)
+    token_usage_records: list[dict[str, int | str | None]] = field(default_factory=list)
     usage_reported: bool = False
     cancel_event: threading.Event = field(default_factory=threading.Event, repr=False)
     _state_lock: threading.Lock = field(default_factory=threading.Lock, init=False, repr=False)
@@ -107,7 +107,7 @@ class SubagentResult:
         error: str | None = None,
         completed_at: datetime | None = None,
         ai_messages: list[dict[str, Any]] | None = None,
-        token_usage_records: list[dict[str, int | str]] | None = None,
+        token_usage_records: list[dict[str, int | str | None]] | None = None,
     ) -> bool:
         """Set a terminal status exactly once.
 
diff --git a/backend/packages/harness/deerflow/subagents/token_collector.py b/backend/packages/harness/deerflow/subagents/token_collector.py
index 56b419f01..54ddcb946 100644
--- a/backend/packages/harness/deerflow/subagents/token_collector.py
+++ b/backend/packages/harness/deerflow/subagents/token_collector.py
@@ -7,6 +7,7 @@ via :meth:`RunJournal.record_external_llm_usage_records`.
 
 from __future__ import annotations
 
+from collections.abc import Mapping
 from typing import Any
 
 from langchain_core.callbacks import BaseCallbackHandler
@@ -18,7 +19,7 @@ class SubagentTokenCollector(BaseCallbackHandler):
     def __init__(self, caller: str):
         super().__init__()
         self.caller = caller
-        self._records: list[dict[str, int | str]] = []
+        self._records: list[dict[str, int | str | None]] = []
         self._counted_run_ids: set[str] = set()
 
     def on_llm_end(
@@ -46,11 +47,19 @@ class SubagentTokenCollector(BaseCallbackHandler):
                     total_tk = input_tk + output_tk
                 if total_tk <= 0:
                     continue
+                # Capture the model that actually produced this response so the
+                # parent journal can bucket tokens by real model rather than the
+                # lead agent's resolved model
+                response_metadata = getattr(gen.message, "response_metadata", None) or {}
+                model_name: str | None = None
+                if isinstance(response_metadata, Mapping):
+                    model_name = response_metadata.get("model_name") or response_metadata.get("model")
                 self._counted_run_ids.add(rid)
                 self._records.append(
                     {
                         "source_run_id": rid,
                         "caller": self.caller,
+                        "model_name": model_name,
                         "input_tokens": input_tk,
                         "output_tokens": output_tk,
                         "total_tokens": total_tk,
@@ -58,6 +67,6 @@ class SubagentTokenCollector(BaseCallbackHandler):
                 )
                 return
 
-    def snapshot_records(self) -> list[dict[str, int | str]]:
+    def snapshot_records(self) -> list[dict[str, int | str | None]]:
         """Return a copy of the accumulated usage records."""
         return list(self._records)
diff --git a/backend/tests/test_run_repository.py b/backend/tests/test_run_repository.py
index 037201f37..7b44cbb93 100644
--- a/backend/tests/test_run_repository.py
+++ b/backend/tests/test_run_repository.py
@@ -3,8 +3,6 @@
 Uses a temp SQLite DB to test ORM-backed CRUD operations.
 """
 
-import re
-
 import pytest
 from sqlalchemy.dialects import postgresql
 
@@ -451,7 +449,11 @@ class TestRunRepository:
         await _cleanup()
 
     @pytest.mark.anyio
-    async def test_aggregate_tokens_by_thread_reuses_shared_model_name_expression(self):
+    async def test_aggregate_tokens_by_thread_returns_zeros_when_no_rows(self):
+        """Empty thread aggregates to all-zero totals, no model buckets, and a
+        single query — replaces the older test that pinned the now-removed
+        ``GROUP BY coalesce(model_name)`` shape (issue #3645 reduces by_model
+        in Python from each row's per-model JSON column instead)."""
         captured = []
 
         class FakeResult:
@@ -483,17 +485,44 @@ class TestRunRepository:
         }
         assert len(captured) == 1
 
-        stmt = captured[0]
-        compiled_sql = str(stmt.compile(dialect=postgresql.dialect()))
-        select_sql, group_by_sql = compiled_sql.split(" GROUP BY ", maxsplit=1)
-        model_expr_pattern = r"coalesce\(runs\.model_name, %\(([^)]+)\)s\)"
+    @pytest.mark.anyio
+    async def test_aggregate_tokens_by_thread_compiles_on_postgres_dialect(self):
+        """Compile-smoke the new SELECT on the postgres dialect.
 
-        select_match = re.search(model_expr_pattern + r" AS model", select_sql)
-        group_by_match = re.fullmatch(model_expr_pattern, group_by_sql.strip())
+        The project ships both SQLite and Postgres backends. The new aggregation
+        projects ``RunRow.token_usage_by_model`` (a JSON column) directly into
+        the row set instead of grouping on a scalar, so the SQL needs to compile
+        cleanly under PG's JSON/JSONB binding too. Pins:
+          * the JSON column is selected by name (PG would otherwise need a
+            ``::jsonb`` cast or coalesce around it)
+          * there is no GROUP BY / aggregate function left (the per-model
+            reduction now happens in Python — see issue #3645)
+        """
 
-        assert select_match is not None
-        assert group_by_match is not None
-        assert select_match.group(1) == group_by_match.group(1)
+        captured = []
+
+        class FakeResult:
+            def all(self):
+                return []
+
+        class FakeSession:
+            async def execute(self, stmt):
+                captured.append(stmt)
+                return FakeResult()
+
+        class FakeSessionContext:
+            async def __aenter__(self):
+                return FakeSession()
+
+            async def __aexit__(self, exc_type, exc, tb):
+                return None
+
+        repo = RunRepository(lambda: FakeSessionContext())
+        await repo.aggregate_tokens_by_thread("t1")
+
+        compiled = str(captured[0].compile(dialect=postgresql.dialect()))
+        assert "token_usage_by_model" in compiled
+        assert "GROUP BY" not in compiled.upper()
 
     @pytest.mark.anyio
     async def test_run_manager_hydrates_store_only_run_from_sql(self, tmp_path):
diff --git a/backend/tests/test_subagent_token_collector.py b/backend/tests/test_subagent_token_collector.py
index 76f003760..549615173 100644
--- a/backend/tests/test_subagent_token_collector.py
+++ b/backend/tests/test_subagent_token_collector.py
@@ -6,11 +6,12 @@ from uuid import uuid4
 from deerflow.subagents.token_collector import SubagentTokenCollector
 
 
-def _make_llm_response(content="Hello", usage=None):
+def _make_llm_response(content="Hello", usage=None, response_metadata=None):
     """Create a mock LLM response with a message."""
     msg = MagicMock()
     msg.content = content
     msg.usage_metadata = usage
+    msg.response_metadata = response_metadata or {}
 
     gen = MagicMock()
     gen.message = msg
@@ -50,6 +51,32 @@ class TestSubagentTokenCollector:
         assert records[0]["total_tokens"] == 150
         assert "source_run_id" in records[0]
 
+    def test_collects_model_name_from_response_metadata(self):
+        collector = SubagentTokenCollector(caller="subagent:test")
+        usage = {"input_tokens": 100, "output_tokens": 50, "total_tokens": 150}
+        collector.on_llm_end(
+            _make_llm_response("Hi", usage=usage, response_metadata={"model_name": "subagent-model"}),
+            run_id=uuid4(),
+        )
+
+        records = collector.snapshot_records()
+
+        assert len(records) == 1
+        assert records[0]["model_name"] == "subagent-model"
+
+    def test_collects_model_name_from_response_metadata_model_fallback(self):
+        collector = SubagentTokenCollector(caller="subagent:test")
+        usage = {"input_tokens": 100, "output_tokens": 50, "total_tokens": 150}
+        collector.on_llm_end(
+            _make_llm_response("Hi", usage=usage, response_metadata={"model": "provider-model"}),
+            run_id=uuid4(),
+        )
+
+        records = collector.snapshot_records()
+
+        assert len(records) == 1
+        assert records[0]["model_name"] == "provider-model"
+
     def test_total_tokens_zero_uses_input_plus_output(self):
         collector = SubagentTokenCollector(caller="subagent:test")
         usage = {"input_tokens": 200, "output_tokens": 100, "total_tokens": 0}
diff --git a/backend/tests/test_token_usage_by_model.py b/backend/tests/test_token_usage_by_model.py
new file mode 100644
index 000000000..7fa6aad62
--- /dev/null
+++ b/backend/tests/test_token_usage_by_model.py
@@ -0,0 +1,431 @@
+"""Per-model token usage regression tests (issue #3645).
+
+Covers the full path that powers ``GET /api/threads/{id}/token-usage``'s
+``by_model`` field:
+
+* ``RunJournal`` capturing each LLM call's real ``response_metadata.model_name``
+  for both the lead agent / middleware path (``on_llm_end``) and the subagent
+  external-records path (``record_external_llm_usage_records``).
+* ``RunJournal.get_completion_data`` exposing the per-model breakdown so it can
+  be threaded into the run store on completion.
+* ``MemoryRunStore`` and ``RunRepository`` (SQLAlchemy) returning the same
+  ``by_model`` shape from ``aggregate_tokens_by_thread``, with the invariant
+  ``sum(by_model[*].tokens) == total_tokens``.
+* Legacy rows written before this fix (``token_usage_by_model`` empty) falling
+  back to the old ``model_name + total_tokens`` attribution instead of being
+  silently dropped.
+"""
+
+from __future__ import annotations
+
+from unittest.mock import MagicMock
+from uuid import uuid4
+
+import pytest
+
+from deerflow.persistence.run import RunRepository
+from deerflow.runtime.events.store.memory import MemoryRunEventStore
+from deerflow.runtime.journal import RunJournal
+from deerflow.runtime.runs.store.memory import MemoryRunStore
+
+# ---------------------------------------------------------------------------
+# Test doubles
+# ---------------------------------------------------------------------------
+
+
+def _make_llm_response(*, usage: dict | None, model_name: str | None = "lead-model"):
+    """Build a minimal LLM response carrying the bits journal/collector read."""
+    msg = MagicMock()
+    msg.type = "ai"
+    msg.content = ""
+    msg.id = f"msg-{id(msg)}"
+    msg.tool_calls = []
+    msg.invalid_tool_calls = []
+    msg.response_metadata = {} if model_name is None else {"model_name": model_name}
+    msg.usage_metadata = usage
+    msg.additional_kwargs = {}
+    msg.name = None
+    msg.model_dump.return_value = {
+        "content": "",
+        "additional_kwargs": {},
+        "response_metadata": msg.response_metadata,
+        "type": "ai",
+        "name": None,
+        "id": msg.id,
+        "tool_calls": [],
+        "invalid_tool_calls": [],
+        "usage_metadata": usage,
+    }
+    gen = MagicMock()
+    gen.message = msg
+    response = MagicMock()
+    response.generations = [[gen]]
+    return response
+
+
+def _journal() -> RunJournal:
+    return RunJournal("r1", "t1", MemoryRunEventStore(), flush_threshold=100)
+
+
+# ---------------------------------------------------------------------------
+# RunJournal: per-call model accounting
+# ---------------------------------------------------------------------------
+
+
+class TestJournalByModel:
+    def test_lead_agent_call_lands_on_real_model(self) -> None:
+        j = _journal()
+        j.on_llm_end(
+            _make_llm_response(usage={"input_tokens": 10, "output_tokens": 5, "total_tokens": 15}, model_name="lead-model"),
+            run_id=uuid4(),
+            parent_run_id=None,
+            tags=["lead_agent"],
+        )
+        data = j.get_completion_data()
+        assert data["token_usage_by_model"] == {
+            "lead-model": {"input_tokens": 10, "output_tokens": 5, "total_tokens": 15},
+        }
+        assert data["lead_agent_tokens"] == 15
+        assert data["total_tokens"] == 15
+
+    def test_middleware_call_lands_on_its_own_model(self) -> None:
+        """A middleware (e.g. title/summarization) on a different model gets its own bucket."""
+        j = _journal()
+        j.on_llm_end(
+            _make_llm_response(usage={"input_tokens": 10, "output_tokens": 5, "total_tokens": 15}, model_name="lead-model"),
+            run_id=uuid4(),
+            parent_run_id=None,
+            tags=["lead_agent"],
+        )
+        j.on_llm_end(
+            _make_llm_response(usage={"input_tokens": 4, "output_tokens": 1, "total_tokens": 5}, model_name="title-model"),
+            run_id=uuid4(),
+            parent_run_id=None,
+            tags=["middleware:title"],
+        )
+        data = j.get_completion_data()
+        assert data["token_usage_by_model"] == {
+            "lead-model": {"input_tokens": 10, "output_tokens": 5, "total_tokens": 15},
+            "title-model": {"input_tokens": 4, "output_tokens": 1, "total_tokens": 5},
+        }
+        assert data["lead_agent_tokens"] == 15
+        assert data["middleware_tokens"] == 5
+
+    def test_missing_model_name_falls_back_to_unknown(self) -> None:
+        j = _journal()
+        j.on_llm_end(
+            _make_llm_response(usage={"input_tokens": 3, "output_tokens": 2, "total_tokens": 5}, model_name=None),
+            run_id=uuid4(),
+            parent_run_id=None,
+            tags=["lead_agent"],
+        )
+        data = j.get_completion_data()
+        assert data["token_usage_by_model"] == {
+            "unknown": {"input_tokens": 3, "output_tokens": 2, "total_tokens": 5},
+        }
+
+    def test_same_model_aggregates_across_calls(self) -> None:
+        j = _journal()
+        for _ in range(2):
+            j.on_llm_end(
+                _make_llm_response(usage={"input_tokens": 7, "output_tokens": 3, "total_tokens": 10}, model_name="lead-model"),
+                run_id=uuid4(),
+                parent_run_id=None,
+                tags=["lead_agent"],
+            )
+        data = j.get_completion_data()
+        assert data["token_usage_by_model"] == {
+            "lead-model": {"input_tokens": 14, "output_tokens": 6, "total_tokens": 20},
+        }
+
+    def test_subagent_external_records_attribute_to_real_model(self) -> None:
+        """The fix's headline behavior: subagent on a different model no longer
+        steals tokens from the lead model bucket."""
+        j = _journal()
+        # Lead emits 10 tokens on lead-model.
+        j.on_llm_end(
+            _make_llm_response(usage={"input_tokens": 6, "output_tokens": 4, "total_tokens": 10}, model_name="lead-model"),
+            run_id=uuid4(),
+            parent_run_id=None,
+            tags=["lead_agent"],
+        )
+        # Subagent ran on subagent-model and reports 25 tokens via the
+        # external-records bridge (the path SubagentTokenCollector uses).
+        j.record_external_llm_usage_records(
+            [
+                {
+                    "source_run_id": "sub-1",
+                    "caller": "subagent:general-purpose",
+                    "model_name": "subagent-model",
+                    "input_tokens": 15,
+                    "output_tokens": 10,
+                    "total_tokens": 25,
+                },
+            ],
+        )
+        data = j.get_completion_data()
+        assert data["token_usage_by_model"] == {
+            "lead-model": {"input_tokens": 6, "output_tokens": 4, "total_tokens": 10},
+            "subagent-model": {"input_tokens": 15, "output_tokens": 10, "total_tokens": 25},
+        }
+        assert data["total_tokens"] == 35
+        # by_caller stays accurate too.
+        assert data["lead_agent_tokens"] == 10
+        assert data["subagent_tokens"] == 25
+        # Invariant the issue calls out: by_model sums to total_tokens.
+        assert sum(b["total_tokens"] for b in data["token_usage_by_model"].values()) == data["total_tokens"]
+
+    def test_subagent_record_without_model_falls_back_to_unknown(self) -> None:
+        j = _journal()
+        j.record_external_llm_usage_records(
+            [
+                {
+                    "source_run_id": "sub-1",
+                    "caller": "subagent:bash",
+                    "input_tokens": 5,
+                    "output_tokens": 2,
+                    "total_tokens": 7,
+                },
+            ],
+        )
+        data = j.get_completion_data()
+        assert data["token_usage_by_model"] == {
+            "unknown": {"input_tokens": 5, "output_tokens": 2, "total_tokens": 7},
+        }
+
+    def test_on_llm_end_dedup_does_not_double_count_model(self) -> None:
+        j = _journal()
+        rid = uuid4()
+        usage = {"input_tokens": 10, "output_tokens": 5, "total_tokens": 15}
+        j.on_llm_end(_make_llm_response(usage=usage, model_name="lead-model"), run_id=rid, parent_run_id=None, tags=["lead_agent"])
+        # Same langchain run_id firing twice (real callbacks do this) must
+        # not inflate either total_tokens or the per-model bucket.
+        j.on_llm_end(_make_llm_response(usage=usage, model_name="lead-model"), run_id=rid, parent_run_id=None, tags=["lead_agent"])
+        data = j.get_completion_data()
+        assert data["total_tokens"] == 15
+        assert data["token_usage_by_model"] == {
+            "lead-model": {"input_tokens": 10, "output_tokens": 5, "total_tokens": 15},
+        }
+
+    def test_external_records_dedup_does_not_double_count_model(self) -> None:
+        j = _journal()
+        record = {
+            "source_run_id": "sub-1",
+            "caller": "subagent:general-purpose",
+            "model_name": "subagent-model",
+            "input_tokens": 15,
+            "output_tokens": 10,
+            "total_tokens": 25,
+        }
+        j.record_external_llm_usage_records([record])
+        j.record_external_llm_usage_records([record])
+        data = j.get_completion_data()
+        assert data["subagent_tokens"] == 25
+        assert data["token_usage_by_model"] == {
+            "subagent-model": {"input_tokens": 15, "output_tokens": 10, "total_tokens": 25},
+        }
+
+    def test_track_tokens_disabled_keeps_by_model_empty(self) -> None:
+        store = MemoryRunEventStore()
+        j = RunJournal("r1", "t1", store, track_token_usage=False, flush_threshold=100)
+        j.on_llm_end(
+            _make_llm_response(usage={"input_tokens": 10, "output_tokens": 5, "total_tokens": 15}, model_name="lead-model"),
+            run_id=uuid4(),
+            parent_run_id=None,
+            tags=["lead_agent"],
+        )
+        j.record_external_llm_usage_records(
+            [{"source_run_id": "sub", "caller": "subagent:x", "model_name": "sub-model", "input_tokens": 1, "output_tokens": 1, "total_tokens": 2}],
+        )
+        data = j.get_completion_data()
+        assert data["token_usage_by_model"] == {}
+        assert data["total_tokens"] == 0
+
+
+# ---------------------------------------------------------------------------
+# Store aggregation: invariants and parity across MemoryRunStore + RunRepository
+# ---------------------------------------------------------------------------
+
+
+_THREAD = "thread-by-model"
+
+
+def _completed_run(
+    run_id: str,
+    *,
+    model_name: str | None,
+    total_tokens: int,
+    lead: int = 0,
+    sub: int = 0,
+    mw: int = 0,
+    by_model: dict | None = None,
+) -> dict:
+    """Shape that both stores accept for completion writes (kwargs to update_run_completion)."""
+    return {
+        "run_id": run_id,
+        "model_name": model_name,
+        "completion": {
+            "status": "success",
+            "total_input_tokens": 0,
+            "total_output_tokens": 0,
+            "total_tokens": total_tokens,
+            "llm_call_count": 1,
+            "lead_agent_tokens": lead,
+            "subagent_tokens": sub,
+            "middleware_tokens": mw,
+            "token_usage_by_model": by_model or {},
+            "message_count": 0,
+        },
+    }
+
+
+async def _seed_run(store, *, run_id: str, model_name: str | None, completion: dict) -> None:
+    await store.put(run_id, thread_id=_THREAD, status="pending", model_name=model_name)
+    await store.update_run_completion(run_id, **completion)
+
+
+_RUN_FIXTURES = [
+    # 1. Run where subagent and middleware ran on different models than lead.
+    _completed_run(
+        "run-1",
+        model_name="lead-model",
+        total_tokens=300,
+        lead=100,
+        sub=150,
+        mw=50,
+        by_model={
+            "lead-model": {"input_tokens": 60, "output_tokens": 40, "total_tokens": 100},
+            "subagent-model": {"input_tokens": 90, "output_tokens": 60, "total_tokens": 150},
+            "middleware-model": {"input_tokens": 30, "output_tokens": 20, "total_tokens": 50},
+        },
+    ),
+    # 2. Another run, lead on a *different* lead model — exercises multi-run merge.
+    _completed_run(
+        "run-2",
+        model_name="lead-model-b",
+        total_tokens=80,
+        lead=80,
+        by_model={
+            "lead-model-b": {"input_tokens": 50, "output_tokens": 30, "total_tokens": 80},
+        },
+    ),
+    # 3. Legacy row written before this fix: empty token_usage_by_model. Must
+    #    fall back to (model_name, total_tokens) instead of disappearing from
+    #    by_model entirely.
+    _completed_run(
+        "run-3",
+        model_name="legacy-model",
+        total_tokens=42,
+        lead=42,
+        by_model={},
+    ),
+]
+
+
+async def _seed_all(store) -> None:
+    for fix in _RUN_FIXTURES:
+        await _seed_run(store, run_id=fix["run_id"], model_name=fix["model_name"], completion=fix["completion"])
+
+
+def _assert_aggregate_shape(agg: dict) -> None:
+    """Pin the contract that powers /api/threads/{id}/token-usage."""
+    # The headline totals stay the simple SUMs.
+    assert agg["total_tokens"] == 300 + 80 + 42
+    assert agg["total_runs"] == 3
+    assert agg["by_caller"] == {
+        "lead_agent": 100 + 80 + 42,
+        "subagent": 150,
+        "middleware": 50,
+    }
+    # The core fix: subagent / middleware models show up in by_model with their
+    # real tokens; the lead-model bucket is NOT inflated with subagent tokens.
+    assert agg["by_model"]["lead-model"] == {"tokens": 100, "runs": 1}
+    assert agg["by_model"]["subagent-model"] == {"tokens": 150, "runs": 1}
+    assert agg["by_model"]["middleware-model"] == {"tokens": 50, "runs": 1}
+    assert agg["by_model"]["lead-model-b"] == {"tokens": 80, "runs": 1}
+    # Legacy fallback path — empty token_usage_by_model maps to the row's
+    # ``model_name`` with the full total_tokens.
+    assert agg["by_model"]["legacy-model"] == {"tokens": 42, "runs": 1}
+    # Invariant from issue #3645.
+    assert sum(b["tokens"] for b in agg["by_model"].values()) == agg["total_tokens"]
+
+
+@pytest.mark.anyio
+async def test_memory_store_by_model_invariant_and_fallback():
+    store = MemoryRunStore()
+    await _seed_all(store)
+    agg = await store.aggregate_tokens_by_thread(_THREAD)
+    _assert_aggregate_shape(agg)
+
+
+async def _make_sql_repo(tmp_path):
+    from deerflow.persistence.engine import get_session_factory, init_engine
+
+    url = f"sqlite+aiosqlite:///{tmp_path / 'by-model.db'}"
+    await init_engine("sqlite", url=url, sqlite_dir=str(tmp_path))
+    return RunRepository(get_session_factory())
+
+
+async def _close_sql_engine() -> None:
+    from deerflow.persistence.engine import close_engine
+
+    await close_engine()
+
+
+@pytest.mark.anyio
+async def test_sql_store_by_model_invariant_and_fallback(tmp_path):
+    repo = await _make_sql_repo(tmp_path)
+    try:
+        await _seed_all(repo)
+        agg = await repo.aggregate_tokens_by_thread(_THREAD)
+        _assert_aggregate_shape(agg)
+    finally:
+        await _close_sql_engine()
+
+
+@pytest.mark.anyio
+async def test_memory_and_sql_stores_agree(tmp_path):
+    """Memory and SQL stores must return byte-identical aggregations so
+    behavior does not silently diverge based on database.backend choice."""
+    mem = MemoryRunStore()
+    sql = await _make_sql_repo(tmp_path)
+    try:
+        await _seed_all(mem)
+        await _seed_all(sql)
+        mem_agg = await mem.aggregate_tokens_by_thread(_THREAD)
+        sql_agg = await sql.aggregate_tokens_by_thread(_THREAD)
+        assert mem_agg == sql_agg
+    finally:
+        await _close_sql_engine()
+
+
+@pytest.mark.anyio
+async def test_include_active_picks_up_running_progress_snapshot(tmp_path):
+    """``update_run_progress`` must persist ``token_usage_by_model`` so the
+    ``include_active=true`` view of /token-usage reflects in-flight tokens."""
+    repo = await _make_sql_repo(tmp_path)
+    try:
+        await repo.put("run-active", thread_id=_THREAD, status="pending")
+        # Transition to running so update_run_progress' status guard fires.
+        await repo.update_status("run-active", "running")
+        await repo.update_run_progress(
+            "run-active",
+            total_tokens=70,
+            total_input_tokens=40,
+            total_output_tokens=30,
+            lead_agent_tokens=70,
+            token_usage_by_model={
+                "lead-model": {"input_tokens": 40, "output_tokens": 30, "total_tokens": 70},
+            },
+        )
+        # Default (completed-only) excludes running runs.
+        completed_only = await repo.aggregate_tokens_by_thread(_THREAD)
+        assert completed_only["total_runs"] == 0
+        assert completed_only["by_model"] == {}
+
+        active = await repo.aggregate_tokens_by_thread(_THREAD, include_active=True)
+        assert active["total_runs"] == 1
+        assert active["by_model"] == {"lead-model": {"tokens": 70, "runs": 1}}
+        assert active["total_tokens"] == 70
+    finally:
+        await _close_sql_engine()