diff --git a/input/input_remapping.c b/input/input_remapping.c
index c3265815b0..a87917fbe1 100644
--- a/input/input_remapping.c
+++ b/input/input_remapping.c
@@ -161,7 +161,22 @@ bool input_remapping_save_file(const char *path)
       {
          fill_pathname_join_delim(key_ident[j], buf,
                key_strings[j], '_', sizeof(key_ident[j]));
-         config_set_int(conf, key_ident[j], settings->input.remap_ids[i][j]);
+
+         /* only save values that have been modified */
+         if(j < RARCH_FIRST_CUSTOM_BIND)
+         {
+            if(settings->input.remap_ids[i][j] != j)
+               config_set_int(conf, key_ident[j], settings->input.remap_ids[i][j]);
+            else
+               config_unset(conf,key_ident[j]);
+         }
+         else
+         {
+            if(settings->input.remap_ids[i][j] != j - RARCH_FIRST_CUSTOM_BIND)
+               config_set_int(conf, key_ident[j], settings->input.remap_ids[i][j]);
+            else
+               config_unset(conf,key_ident[j]);
+         }
       }
 
       for (i = 0; i < MAX_USERS; i++)
diff --git a/libretro-common/file/config_file.c b/libretro-common/file/config_file.c
index 1b0e730cef..dabbbe952d 100644
--- a/libretro-common/file/config_file.c
+++ b/libretro-common/file/config_file.c
@@ -773,6 +773,20 @@ void config_set_string(config_file_t *conf, const char *key, const char *val)
       conf->entries = entry;
 }
 
+void config_unset(config_file_t *conf, const char *key)
+{
+   struct config_entry_list *last  = conf->entries;
+   struct config_entry_list *entry = config_get_entry(conf, key, &last);
+
+   if (!entry)
+      return;
+
+   entry->key   = NULL;
+   entry->value = NULL;
+   free(entry->key);
+   free(entry->value);
+}
+
 void config_set_path(config_file_t *conf, const char *entry, const char *val)
 {
 #if defined(RARCH_CONSOLE)
@@ -873,7 +887,7 @@ void config_file_dump(config_file_t *conf, FILE *file)
    list = (struct config_entry_list*)conf->entries;
    while (list)
    {
-      if (!list->readonly)
+      if (!list->readonly && list->key)
          fprintf(file, "%s = \"%s\"\n", list->key, list->value);
       list = list->next;
    }
diff --git a/libretro-common/include/file/config_file.h b/libretro-common/include/file/config_file.h
index 161ec41022..81baca941c 100644
--- a/libretro-common/include/file/config_file.h
+++ b/libretro-common/include/file/config_file.h
@@ -147,6 +147,7 @@ void config_set_hex(config_file_t *conf, const char *entry, unsigned val);
 void config_set_uint64(config_file_t *conf, const char *entry, uint64_t val);
 void config_set_char(config_file_t *conf, const char *entry, char val);
 void config_set_string(config_file_t *conf, const char *entry, const char *val);
+void config_unset(config_file_t *conf, const char *key);
 void config_set_path(config_file_t *conf, const char *entry, const char *val);
 void config_set_bool(config_file_t *conf, const char *entry, bool val);