diff --git a/pkgs/development/interpreters/python/mk-python-derivation.nix b/pkgs/development/interpreters/python/mk-python-derivation.nix
index f3e5249c189e3..0fb0a1326025c 100644
--- a/pkgs/development/interpreters/python/mk-python-derivation.nix
+++ b/pkgs/development/interpreters/python/mk-python-derivation.nix
@@ -418,6 +418,7 @@ lib.extendMkDerivation {
           optional-dependencies
           ;
         updateScript = nix-update-script { };
+        ${if attrs ? stdenv then "__stdenvPythonCompat" else null} = attrs.stdenv;
       }
       // attrs.passthru or { };
 
diff --git a/pkgs/development/interpreters/python/python-packages-base.nix b/pkgs/development/interpreters/python/python-packages-base.nix
index 91d733a33c3e5..16c68c47c4b97 100644
--- a/pkgs/development/interpreters/python/python-packages-base.nix
+++ b/pkgs/development/interpreters/python/python-packages-base.nix
@@ -24,10 +24,24 @@ let
       let
         result = f origArgs;
         overrideWith =
+          # Preserve the plain arguments whenever possible,
+          # as `overrideStdenvCompat` works more reliably with `args.stdenv`
+          # than `result.__stdenvPythonCompat`.
+          # TODO(@ShamrockLee): After `overrideStdenvCompat` is fully deprecated,
+          # simplify as
+          # ```nix
+          # newArgs: lib.extends (lib.toExtension newArgs) origArgs
+          # ```
           if lib.isFunction origArgs then
-            newArgs: lib.extends (_: lib.toFunction newArgs) origArgs
+            newArgs: lib.extends (lib.toExtension newArgs) origArgs
           else
-            newArgs: origArgs // lib.toFunction newArgs origArgs;
+            newArgs:
+            if !(lib.isFunction newArgs) then
+              origArgs // newArgs
+            else if !(lib.isFunction (newArgs origArgs)) then
+              origArgs // newArgs origArgs
+            else
+              finalAttrs: origArgs // newArgs finalAttrs origArgs;
       in
       if lib.isAttrs result then
         result
@@ -53,15 +67,21 @@ let
       f':
       lib.mirrorFunctionArgs f (
         args:
-        if !(lib.isFunction args) && (args ? stdenv) then
-          lib.warnIf (lib.oldestSupportedReleaseIsAtLeast 2511) ''
+        let
+          result = f args;
+          applyMsgStdenvArg = lib.warnIf (lib.oldestSupportedReleaseIsAtLeast 2511) ''
             ${
               args.name or args.pname or "<unnamed>"
             }: Passing `stdenv` directly to `buildPythonPackage` or `buildPythonApplication` is deprecated. You should use their `.override` function instead, e.g:
               buildPythonPackage.override { stdenv = customStdenv; } { }
-          '' (f'.override { inherit (args) stdenv; } (removeAttrs args [ "stdenv" ]))
+          '';
+        in
+        if !(lib.isFunction args) && (args ? stdenv) then
+          f'.override { stdenv = applyMsgStdenvArg args.stdenv; } (removeAttrs args [ "stdenv" ])
+        else if result ? __stdenvPythonCompat then
+          f'.override { stdenv = applyMsgStdenvArg result.__stdenvPythonCompat; } args
         else
-          f args
+          result
       )
       // {
         # Preserve the effect of overrideStdenvCompat when calling `buildPython*.override`.
diff --git a/pkgs/test/overriding.nix b/pkgs/test/overriding.nix
index 9d2d0612d23ab..05f585a638834 100644
--- a/pkgs/test/overriding.nix
+++ b/pkgs/test/overriding.nix
@@ -424,6 +424,14 @@ let
         p.overridePythonAttrs (previousAttrs: {
           overridePythonAttrsFlag = previousAttrs.overridePythonAttrsFlag or 0 + 1;
         });
+      applyOverridePythonAttrsFP =
+        p:
+        p.overridePythonAttrs (
+          finalAttrs: previousAttrs: {
+            overridePythonAttrsFlag = previousAttrs.overridePythonAttrsFlag or 0 + 1;
+            overridePythonAttrsFlagP1 = finalAttrs.overridePythonAttrsFlag + 1;
+          }
+        );
       overrideAttrsFooBar =
         drv:
         drv.overrideAttrs (
@@ -455,6 +463,22 @@ let
         expr = (applyOverridePythonAttrs (applyOverridePythonAttrs package-stub)).overridePythonAttrsFlag;
         expected = 2;
       };
+      overridePythonAttrs-plain = {
+        expr = (package-stub.overridePythonAttrs { overridePythonAttrsFlag = 0; }).overridePythonAttrsFlag;
+        expected = 0;
+      };
+      overridePythonAttrs-finalAttrs = {
+        expr = {
+          inherit (applyOverridePythonAttrsFP package-stub)
+            overridePythonAttrsFlag
+            overridePythonAttrsFlagP1
+            ;
+        };
+        expected = {
+          overridePythonAttrsFlag = 1;
+          overridePythonAttrsFlagP1 = 2;
+        };
+      };
       overrideAttrs-overridePythonAttrs-test-overrideAttrs = {
         expr = {
           inherit (applyOverridePythonAttrs (overrideAttrsFooBar package-stub))