diff --git a/apps/backend/backend_commit.c b/apps/backend/backend_commit.c
index 6a89dc0b..d3177d84 100644
--- a/apps/backend/backend_commit.c
+++ b/apps/backend/backend_commit.c
@@ -749,7 +749,9 @@ candidate_commit(clixon_handle  h,
     /* Remove system-only-config data from destination cache */
     if (clicon_option_bool(h, "CLICON_XMLDB_SYSTEM_ONLY_CONFIG")){
         xmldb_clear(h, "running");
+#ifdef SYSTEM_ONLY_CONFIG_CANDIDATE_CLEAR
         xmldb_clear(h, db);
+#endif
     }
     xmldb_modified_set(h, db, 0); /* reset dirty bit */
     /* Here pointers to old (source) tree are obsolete */
diff --git a/include/clixon_custom.h b/include/clixon_custom.h
index 981af158..ca386f7c 100644
--- a/include/clixon_custom.h
+++ b/include/clixon_custom.h
@@ -204,3 +204,13 @@
  * If not set, reduces memory with 8 bytes per yang-stmt.
  */
 #undef YANG_SPEC_LINENR
+
+/*! Effort to clear system-only config data from candidate cache after commit
+ *
+ * The idea was that the candidate would be re-loaded from file and populated (as running)
+ * However, there may be instances where the candidate cache is loaded without YANG binding,
+ * such as in xmldb_get0(h, "candidate", YB_NONE,...), whereas running cache is loaded with YANG.
+ * This causes xml_cmp to show that the datastores are unequal and may cause a wrong diff, or
+ * worse case an overwrite.
+ */
+#undef SYSTEM_ONLY_CONFIG_CANDIDATE_CLEAR