diff --git a/platformio/check/cli.py b/platformio/check/cli.py
index 3e0c1759..9adf7fb9 100644
--- a/platformio/check/cli.py
+++ b/platformio/check/cli.py
@@ -103,10 +103,21 @@ def cli(
                     "%s: %s" % (k, ", ".join(v) if isinstance(v, list) else v)
                 )
 
-            default_src_filters = [
-                "+<%s>" % os.path.basename(config.get("platformio", "src_dir")),
-                "+<%s>" % os.path.basename(config.get("platformio", "include_dir")),
-            ]
+            default_src_filters = []
+            for d in (
+                config.get("platformio", "src_dir"),
+                config.get("platformio", "include_dir"),
+            ):
+                try:
+                    default_src_filters.append("+<%s>" % os.path.relpath(d))
+                except ValueError as exc:
+                    # On Windows if sources are located on a different logical drive
+                    if not json_output and not silent:
+                        click.echo(
+                            "Error: Project cannot be analyzed! The project folder `%s`"
+                            " is located on a different logical drive\n" % d
+                        )
+                    raise exception.ReturnErrorCode(1) from exc
 
             env_src_filters = (
                 src_filters
diff --git a/tests/commands/test_check.py b/tests/commands/test_check.py
index a9a99d65..5f32e77d 100644
--- a/tests/commands/test_check.py
+++ b/tests/commands/test_check.py
@@ -803,3 +803,49 @@ check_src_filters =
     assert errors + warnings + style == EXPECTED_DEFECTS
     assert "test.cpp" in result.output
     assert "main.cpp" not in result.output
+
+
+def test_check_sources_in_project_root(clirunner, validate_cliresult, tmpdir_factory):
+    tmpdir = tmpdir_factory.mktemp("project")
+
+    config = (
+        """
+[platformio]
+src_dir = ./
+    """
+        + DEFAULT_CONFIG
+    )
+    tmpdir.join("platformio.ini").write(config)
+    tmpdir.join("main.cpp").write(TEST_CODE)
+    tmpdir.mkdir("spi").join("uart.cpp").write(TEST_CODE)
+
+    result = clirunner.invoke(cmd_check, ["--project-dir", str(tmpdir)])
+    validate_cliresult(result)
+
+    errors, warnings, style = count_defects(result.output)
+
+    assert result.exit_code == 0
+    assert errors + warnings + style == EXPECTED_DEFECTS * 2
+
+
+def test_check_sources_in_external_dir(clirunner, validate_cliresult, tmpdir_factory):
+    tmpdir = tmpdir_factory.mktemp("project")
+    external_src_dir = tmpdir_factory.mktemp("external_src_dir")
+
+    config = (
+        f"""
+[platformio]
+src_dir = {external_src_dir}
+    """
+        + DEFAULT_CONFIG
+    )
+    tmpdir.join("platformio.ini").write(config)
+    external_src_dir.join("main.cpp").write(TEST_CODE)
+
+    result = clirunner.invoke(cmd_check, ["--project-dir", str(tmpdir)])
+    validate_cliresult(result)
+
+    errors, warnings, style = count_defects(result.output)
+
+    assert result.exit_code == 0
+    assert errors + warnings + style == EXPECTED_DEFECTS