diff --git a/tests/scripts/all.sh b/tests/scripts/all.sh
index 016aa0062..2d52fd13d 100755
--- a/tests/scripts/all.sh
+++ b/tests/scripts/all.sh
@@ -137,6 +137,8 @@ pre_initialize_variables () {
     backup_suffix='.all.bak'
     # Files clobbered by config.py
     files_to_back_up="$CONFIG_H $CRYPTO_CONFIG_H"
+    # Files clobbered by in-tree cmake
+    files_to_back_up="$files_to_back_up Makefile library/Makefile programs/Makefile tests/Makefile programs/fuzz/Makefile"
 
     append_outcome=0
     MEMORY=0
@@ -286,8 +288,6 @@ cleanup()
               -iname CMakeCache.txt \) -exec rm {} \+
     # Recover files overwritten by in-tree CMake builds
     rm -f include/Makefile include/mbedtls/Makefile programs/*/Makefile
-    git update-index --no-skip-worktree Makefile library/Makefile programs/Makefile tests/Makefile programs/fuzz/Makefile
-    git checkout -- Makefile library/Makefile programs/Makefile tests/Makefile programs/fuzz/Makefile
 
     # Remove any artifacts from the component_test_cmake_as_subdirectory test.
     rm -rf programs/test/cmake_subproject/build
@@ -490,6 +490,20 @@ pre_check_git () {
     fi
 }
 
+pre_restore_files () {
+    # If the makefiles have been generated by a framework such as cmake,
+    # restore them from git. If the makefiles look like modifications from
+    # the ones checked into git, take care not to modify them. Whatever
+    # this function leaves behind is what the script will restore before
+    # each component.
+    case "$(head -n1 Makefile)" in
+        *[Gg]enerated*)
+            git update-index --no-skip-worktree Makefile library/Makefile programs/Makefile tests/Makefile programs/fuzz/Makefile
+            git checkout -- Makefile library/Makefile programs/Makefile tests/Makefile programs/fuzz/Makefile
+            ;;
+    esac
+}
+
 pre_back_up () {
     for x in $files_to_back_up; do
         cp -p "$x" "$x$backup_suffix"
@@ -2921,6 +2935,7 @@ pre_initialize_variables
 pre_parse_command_line "$@"
 
 pre_check_git
+pre_restore_files
 pre_back_up
 
 build_status=0