diff --git a/newsfragments/4790.feature.rst b/newsfragments/4790.feature.rst
new file mode 100644
index 0000000000..21139708b3
--- /dev/null
+++ b/newsfragments/4790.feature.rst
@@ -0,0 +1 @@
+Synced with pypa/distutils@ff11eed0c including bugfix for duplicate CFLAGS and adaption to support Python 3.13 is_abs in the C compiler (#4669).
diff --git a/setuptools/_distutils/ccompiler.py b/setuptools/_distutils/ccompiler.py
index 5e73e56d02..714f13d8d3 100644
--- a/setuptools/_distutils/ccompiler.py
+++ b/setuptools/_distutils/ccompiler.py
@@ -4,6 +4,7 @@
 for the Distutils compiler abstraction model."""
 
 import os
+import pathlib
 import re
 import sys
 import types
@@ -969,27 +970,33 @@ def out_extensions(self):
         return dict.fromkeys(self.src_extensions, self.obj_extension)
 
     def _make_out_path(self, output_dir, strip_dir, src_name):
-        base, ext = os.path.splitext(src_name)
-        base = self._make_relative(base)
+        return self._make_out_path_exts(
+            output_dir, strip_dir, src_name, self.out_extensions
+        )
+
+    @classmethod
+    def _make_out_path_exts(cls, output_dir, strip_dir, src_name, extensions):
+        r"""
+        >>> exts = {'.c': '.o'}
+        >>> CCompiler._make_out_path_exts('.', False, '/foo/bar.c', exts).replace('\\', '/')
+        './foo/bar.o'
+        >>> CCompiler._make_out_path_exts('.', True, '/foo/bar.c', exts).replace('\\', '/')
+        './bar.o'
+        """
+        src = pathlib.PurePath(src_name)
+        # Ensure base is relative to honor output_dir (python/cpython#37775).
+        base = cls._make_relative(src)
         try:
-            new_ext = self.out_extensions[ext]
+            new_ext = extensions[src.suffix]
         except LookupError:
-            raise UnknownFileError(f"unknown file type '{ext}' (from '{src_name}')")
+            raise UnknownFileError(f"unknown file type '{src.suffix}' (from '{src}')")
         if strip_dir:
-            base = os.path.basename(base)
-        return os.path.join(output_dir, base + new_ext)
+            base = pathlib.PurePath(base.name)
+        return os.path.join(output_dir, base.with_suffix(new_ext))
 
     @staticmethod
-    def _make_relative(base):
-        """
-        In order to ensure that a filename always honors the
-        indicated output_dir, make sure it's relative.
-        Ref python/cpython#37775.
-        """
-        # Chop off the drive
-        no_drive = os.path.splitdrive(base)[1]
-        # If abs, chop off leading /
-        return no_drive[os.path.isabs(no_drive) :]
+    def _make_relative(base: pathlib.Path):
+        return base.relative_to(base.anchor)
 
     def shared_object_filename(self, basename, strip_dir=False, output_dir=''):
         assert output_dir is not None
diff --git a/setuptools/_distutils/sysconfig.py b/setuptools/_distutils/sysconfig.py
index 358d1079dc..ef3def83eb 100644
--- a/setuptools/_distutils/sysconfig.py
+++ b/setuptools/_distutils/sysconfig.py
@@ -341,7 +341,6 @@ def customize_compiler(compiler):
         ldshared = _add_flags(ldshared, 'LD')
         ldcxxshared = _add_flags(ldcxxshared, 'LD')
         cflags = os.environ.get('CFLAGS', cflags)
-        cflags = _add_flags(cflags, 'C')
         ldshared = _add_flags(ldshared, 'C')
         cxxflags = os.environ.get('CXXFLAGS', cxxflags)
         ldcxxshared = _add_flags(ldcxxshared, 'CXX')
diff --git a/setuptools/_distutils/tests/test_ccompiler.py b/setuptools/_distutils/tests/test_ccompiler.py
index d23b907cad..7ebfed56be 100644
--- a/setuptools/_distutils/tests/test_ccompiler.py
+++ b/setuptools/_distutils/tests/test_ccompiler.py
@@ -7,6 +7,8 @@
 
 import pytest
 
+pytestmark = pytest.mark.usefixtures('suppress_path_mangle')
+
 
 def _make_strs(paths):
     """
diff --git a/setuptools/_distutils/tests/test_sysconfig.py b/setuptools/_distutils/tests/test_sysconfig.py
index 867e7dcb39..43d77c23fa 100644
--- a/setuptools/_distutils/tests/test_sysconfig.py
+++ b/setuptools/_distutils/tests/test_sysconfig.py
@@ -130,11 +130,9 @@ def test_customize_compiler(self):
         comp = self.customize_compiler()
         assert comp.exes['archiver'] == 'env_ar --env-arflags'
         assert comp.exes['preprocessor'] == 'env_cpp --env-cppflags'
-        assert (
-            comp.exes['compiler'] == 'env_cc --env-cflags --env-cflags --env-cppflags'
-        )
+        assert comp.exes['compiler'] == 'env_cc --env-cflags --env-cppflags'
         assert comp.exes['compiler_so'] == (
-            'env_cc --env-cflags --env-cflags --env-cppflags --sc-ccshared'
+            'env_cc --env-cflags --env-cppflags --sc-ccshared'
         )
         assert (
             comp.exes['compiler_cxx']