diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a2f304aa5..d18f53df9 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -89,12 +89,18 @@ jobs:
             exit 1
           fi
 
-      - name: Run tests
+      - name: Run unit tests
         env:
           RUST_BACKTRACE: 1
         run: |
           git submodule update --init
-          uv run --no-project pytest -v --import-mode=importlib
+          uv run --no-project pytest -v --import-mode=importlib python/tests
+
+      - name: Run doctests
+        env:
+          RUST_BACKTRACE: 1
+        run: |
+          uv run --no-project pytest -v --import-mode=importlib --doctest-modules python/datafusion
 
       - name: FFI unit tests
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index 117aeefc2..c2c5a93dc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -71,7 +71,6 @@ features = ["substrait"]
 [tool.pytest.ini_options]
 asyncio_mode = "auto"
 asyncio_default_fixture_loop_scope = "function"
-addopts = "--doctest-modules"
 doctest_optionflags = ["NORMALIZE_WHITESPACE", "ELLIPSIS"]
 testpaths = ["python/tests", "python/datafusion"]