diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 471cf190fb..0b887a2cdb 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -836,7 +836,7 @@ (define-public python-3.12
                                          "json/tests"
                                          "distutils/tests"))))))))
                   (add-after 'remove-tests 'move-tk-inter
-                    (lambda* (#:key outputs #:allow-other-keys)
+                    (lambda* (#:key outputs inputs #:allow-other-keys)
                       ;; When Tkinter support is built move it to a separate output so
                       ;; that the main output doesn't contain a reference to Tcl/Tk.
                       (let ((out (assoc-ref outputs "out"))
@@ -854,7 +854,14 @@ (define-public python-3.12
                                                                         len)
                                                            "/site-packages")))
                                (install-file tkinter.so target)
-                               (delete-file tkinter.so))))))))
+                               (delete-file tkinter.so))))
+                          ;; Remove explicit store path references.
+                          (let ((tcl (assoc-ref inputs "tcl"))
+                                (tk (assoc-ref inputs "tk")))
+                            (substitute* (find-files (string-append out "/lib")
+                                                     "^(_sysconfigdata_.*\\.py|Makefile)$")
+                                         (((string-append "-L" tk "/lib")) "")
+                                         (((string-append "-L" tcl "/lib")) "")))))))
                   (add-after 'move-tk-inter 'move-idle
                     (lambda* (#:key outputs #:allow-other-keys)
                       ;; when idle is built, move it to a separate output to save some