diff --git a/src/cppboot/generate/cmake_files.py b/src/cppboot/generate/cmake_files.py
index c00f3a8..e2ad060 100644
--- a/src/cppboot/generate/cmake_files.py
+++ b/src/cppboot/generate/cmake_files.py
@@ -418,11 +418,17 @@ def _src_cmake(ctx: _Context) -> str:
 
 def _version_src_cmake(ctx: _Context) -> str:
     if ctx.with_modules:
+        # BASE_DIRS must include the generated .cppm path; CMake rejects FILE_SET
+        # members outside the set's base directories (often defaults to this dir).
         return f"""\
 # version component (C++20 module) — generated from cmake/version.cppm.in + VERSION.
+# Generated unit lives under the build tree; BASE_DIRS must cover that path.
 target_sources(${{PROJECT_NAME}}_lib
   PUBLIC
-    FILE_SET CXX_MODULES FILES
+    FILE_SET CXX_MODULES
+    BASE_DIRS
+      ${{{ctx.macro}_GENERATED_DIR}}
+    FILES
       ${{{ctx.macro}_GENERATED_DIR}}/version.cppm
 )
 """
diff --git a/tests/integration/test_generate.py b/tests/integration/test_generate.py
index a371021..003aaa6 100644
--- a/tests/integration/test_generate.py
+++ b/tests/integration/test_generate.py
@@ -107,6 +107,13 @@ def test_modules_layout(tmp_root: Path) -> None:
     assert not (root / "cmake" / "version.hpp.in").exists()
     cmake = (root / "CMakeLists.txt").read_text(encoding="utf-8")
     assert "3.28" in cmake
+    version_cmake = (root / "src" / "version" / "CMakeLists.txt").read_text(encoding="utf-8")
+    assert "FILE_SET CXX_MODULES" in version_cmake
+    assert "BASE_DIRS" in version_cmake
+    assert "version.cppm" in version_cmake
+    main = (root / "src" / "main.cpp").read_text(encoding="utf-8")
+    assert "import " in main
+    assert "#include" not in main or "CLI" in main  # CLI11 still classic header
 
 
 def test_shared_library(tmp_root: Path) -> None: