diff --git a/platformio/builder/tools/piobuild.py b/platformio/builder/tools/piobuild.py
index 23d0c6ff..6fb2eb6f 100644
--- a/platformio/builder/tools/piobuild.py
+++ b/platformio/builder/tools/piobuild.py
@@ -201,13 +201,13 @@ def ParseFlagsExtended(env, flags):  # pylint: disable=too-many-branches
     for k in ("CPPPATH", "LIBPATH"):
         for i, p in enumerate(result.get(k, [])):
             p = env.subst(p)
-            result[k][i] = p if os.path.isabs(p) else env.Dir(f"#{p}")
+            if os.path.isdir(p):
+                result[k][i] = os.path.abspath(p)
 
     # fix relative path for "-include"
     for i, f in enumerate(result.get("CCFLAGS", [])):
         if isinstance(f, tuple) and f[0] == "-include":
-            p = env.subst(f[1].get_path())
-            result["CCFLAGS"][i] = (f[0], p if os.path.isabs(p) else env.File(f"#{p}"))
+            result["CCFLAGS"][i] = (f[0], env.subst(f[1].get_path()))
 
     return result
 
diff --git a/tests/commands/test_run.py b/tests/commands/test_run.py
index 573ac9ef..820de44f 100644
--- a/tests/commands/test_run.py
+++ b/tests/commands/test_run.py
@@ -25,7 +25,7 @@ def test_generic_build(clirunner, validate_cliresult, tmpdir):
         ("-Iinclude", "-Iinclude"),
         ("-include cpppath-include.h", "cpppath-include.h"),
         ("-Iextra_inc", "-Iextra_inc"),
-        ("-Inon-existing-dir", "-Inon-existing-dir"),
+        ("-Inon-existing-dir", "non-existing-dir"),
         (
             "-include $PROJECT_DIR/lib/component/component-forced-include.h",
             "component-forced-include.h",