diff --git a/Misc/NEWS.d/next/Build/2024-10-13-21-11-30.gh-issue-125269.BC-fdo.rst b/Misc/NEWS.d/next/Build/2024-10-13-21-11-30.gh-issue-125269.BC-fdo.rst
new file mode 100644
index 00000000000..24f5469e8a6
--- /dev/null
+++ b/Misc/NEWS.d/next/Build/2024-10-13-21-11-30.gh-issue-125269.BC-fdo.rst
@@ -0,0 +1,2 @@
+Fix detection of whether ``-latomic`` is needed when cross-compiling CPython
+using the configure script.
diff --git a/configure b/configure
index c5bec6a1b0d..be119f108a0 100755
--- a/configure
+++ b/configure
@@ -28999,10 +28999,6 @@ printf %s "checking whether libatomic is needed by <pyatomic.h>... " >&6; }
 if test ${ac_cv_libatomic_needed+y}
 then :
   printf %s "(cached) " >&6
-else $as_nop
-  if test "$cross_compiling" = yes
-then :
-    ac_cv_libatomic_needed=no
 else $as_nop
   cat confdefs.h - <<_ACEOF >conftest.$ac_ext
 /* end confdefs.h.  */
@@ -29044,16 +29040,14 @@ int main()
 }
 
 _ACEOF
-if ac_fn_c_try_run "$LINENO"
+if ac_fn_c_try_link "$LINENO"
 then :
   ac_cv_libatomic_needed=no
 else $as_nop
     ac_cv_libatomic_needed=yes
 fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
-  conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-
+rm -f core conftest.err conftest.$ac_objext conftest.beam \
+    conftest$ac_exeext conftest.$ac_ext
 fi
 { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $ac_cv_libatomic_needed" >&5
 printf "%s\n" "$ac_cv_libatomic_needed" >&6; }
diff --git a/configure.ac b/configure.ac
index d4b79421902..582851695e4 100644
--- a/configure.ac
+++ b/configure.ac
@@ -7497,7 +7497,7 @@ CPPFLAGS="${BASECPPFLAGS} -I. -I${srcdir}/Include ${CPPFLAGS}"
 
 AC_CACHE_CHECK([whether libatomic is needed by <pyatomic.h>],
                [ac_cv_libatomic_needed],
-[AC_RUN_IFELSE([AC_LANG_SOURCE([[
+[AC_LINK_IFELSE([AC_LANG_SOURCE([[
 // pyatomic.h needs uint64_t and Py_ssize_t types
 #include <stdint.h>  // int64_t, intptr_t
 #ifdef HAVE_SYS_TYPES_H
@@ -7534,9 +7534,8 @@ int main()
     return 0; // all good
 }
 ]])],
-  [ac_cv_libatomic_needed=no],  dnl build succeeded
-  [ac_cv_libatomic_needed=yes], dnl build failed
-  [ac_cv_libatomic_needed=no])  dnl cross compilation
+  [ac_cv_libatomic_needed=no],  dnl build and link succeeded
+  [ac_cv_libatomic_needed=yes]) dnl build and link failed
 ])
 
 AS_VAR_IF([ac_cv_libatomic_needed], [yes],