diff --git a/docs/REFERENCE-cmake.md b/docs/REFERENCE-cmake.md
index 49ed665..1d2155a 100644
--- a/docs/REFERENCE-cmake.md
+++ b/docs/REFERENCE-cmake.md
@@ -48,6 +48,11 @@ aquery must mirror.
 
 - **Target names** in `target_map` and `exclude_targets` keys are CMake target
   names (e.g. `"bssl": ":bssl"`).
+- **Project in a subdirectory**: `cmake -S` may be any directory under
+  `<repo_root>` (e.g. one CMake project per firmware image inside a larger
+  Bazel workspace). The File API reports in-tree sources relative to that
+  top-level source dir; the extractor resolves them against the codemodel's
+  `paths.source`, so TU keys stay relative to `<repo_root>`.
 - **`dep_map`**: CMake spells external link deps as an archive basename
   (`Catch2Main`) or an imported target (`OpenSSL::SSL`), while Bazel spells them
   `catch2_main` / `ssl`.
diff --git a/scripts/extract_cmake.py b/scripts/extract_cmake.py
index f070f1f..4e6b451 100644
--- a/scripts/extract_cmake.py
+++ b/scripts/extract_cmake.py
@@ -29,7 +29,8 @@
     python3 extract_cmake.py <build> <repo_root> model.cmake.json
 
 The reply lands in <build>/.cmake/api/v1/reply/. We read the codemodel index,
-then each per-target jsonFile.
+then each per-target jsonFile. <src> may be <repo_root> or any directory under
+it: source paths are resolved against the codemodel's top-level source dir.
 """
 
 from __future__ import annotations
@@ -139,10 +140,14 @@ def _target_id_to_name(codemodel: dict) -> Dict[str, str]:
     return out
 
 
-def _parse_target(tobj: dict, repo_root: str) -> Target:
+def _parse_target(tobj: dict, source_dir: str) -> Target:
     name = tobj["name"]
     kind = _KIND.get(tobj.get("type", ""), TargetKind.UNKNOWN)
-    sources = [s["path"] for s in tobj.get("sources", [])]
+    # The File API gives sources inside the top-level source dir relative to IT
+    # (not to repo_root, which differs when `cmake -S` is a subdirectory), and
+    # others absolute. Make them all absolute so they key repo-relative later.
+    sources = [os.path.normpath(os.path.join(source_dir, s["path"]))
+               for s in tobj.get("sources", [])]
 
     # Synthesize one CppCompile Action per source: an argv the differ parses the
     # same way it parses Bazel's. CMake has no real command line, so we build the
@@ -230,6 +235,8 @@ def extract(build_dir: str, repo_root: str,
     reply_dir = os.path.join(build_dir, ".cmake", "api", "v1", "reply")
     codemodel = _find_codemodel(reply_dir)
     id_to_name = _target_id_to_name(codemodel)
+    # top-level source dir (`cmake -S`); may be any directory under repo_root
+    source_dir = codemodel.get("paths", {}).get("source") or repo_root
 
     model = CanonicalModel(build_system=BuildSystem.CMAKE, repo_root=repo_root)
     include_dirs = set()
@@ -237,7 +244,7 @@ def extract(build_dir: str, repo_root: str,
     for tref in cfg["targets"]:
         with open(os.path.join(reply_dir, tref["jsonFile"])) as f:
             tobj = json.load(f)
-        target = _parse_target(tobj, repo_root)
+        target = _parse_target(tobj, source_dir)
         _attach_deps(target, tobj, id_to_name)
         model.add(target)
         for cg in tobj.get("compileGroups", []):
diff --git a/tests/test_extractors.py b/tests/test_extractors.py
index fd282b7..82b62bd 100644
--- a/tests/test_extractors.py
+++ b/tests/test_extractors.py
@@ -104,15 +104,15 @@ def _view(model, name):
 }
 
 
-def _write_cmake_fixture(root):
+def _write_cmake_fixture(root, codemodel=CODEMODEL, target=TARGET_MYLIB):
     reply = os.path.join(root, "build", ".cmake", "api", "v1", "reply")
     os.makedirs(reply)
     with open(os.path.join(reply, "index-0.json"), "w") as f:
         json.dump({"objects": [{"kind": "codemodel", "jsonFile": "codemodel.json"}]}, f)
     with open(os.path.join(reply, "codemodel.json"), "w") as f:
-        json.dump(CODEMODEL, f)
+        json.dump(codemodel, f)
     with open(os.path.join(reply, "target-mylib.json"), "w") as f:
-        json.dump(TARGET_MYLIB, f)
+        json.dump(target, f)
     return os.path.join(root, "build")
 
 
@@ -150,6 +150,26 @@ def test_cmake_extracts_canonical_flags():
         assert "-std=c++17" in tu.flags
 
 
+def test_cmake_sources_resolve_against_top_level_source_dir():
+    # `cmake -S sub/proj` with repo_root one level up: the File API gives
+    # in-tree sources relative to the TOP-LEVEL SOURCE DIR (paths.source), not
+    # to repo_root, and out-of-tree sources absolute. TU keys must still be
+    # repo-relative, else every source looks missing/extra against Bazel.
+    codemodel = dict(CODEMODEL, paths={"source": REPO + "/sub/proj",
+                                       "build": REPO + "/sub/proj/build"})
+    target = dict(TARGET_MYLIB,
+                  sources=[{"path": "src/a.cpp"}, {"path": "/opt/sdk/s.c"}],
+                  compileGroups=[dict(TARGET_MYLIB["compileGroups"][0],
+                                      sourceIndexes=[0, 1])])
+    with tempfile.TemporaryDirectory() as root:
+        build = _write_cmake_fixture(root, codemodel, target)
+        a = extract_cmake.extract(build, REPO)
+        tus = _view(a, "mylib").tu_map()
+        assert sorted(tus) == ["/opt/sdk/s.c", "sub/proj/src/a.cpp"], sorted(tus)
+        compile_inputs = [act.inputs for act in a.targets["mylib"].actions]
+        assert (REPO + "/sub/proj/src/a.cpp",) in compile_inputs, compile_inputs
+
+
 def test_bazel_infers_kind_and_drops_defaults():
     with tempfile.TemporaryDirectory() as root:
         aq_path = os.path.join(root, "aquery.json")