diff --git a/src/main.c b/src/main.c
index eaf8026..083a28f 100644
--- a/src/main.c
+++ b/src/main.c
@@ -50,10 +50,12 @@ static gboolean send_apply(gpointer data) {
   struct wl_display *wl_display = gdk_wayland_display_get_wl_display(display);
   wd_apply_state(state, outputs, wl_display);
   state->apply_pending = FALSE;
+  state->apply_manual = false;
   return FALSE;
 }
 
-static void apply_state(struct wd_state *state) {
+static void apply_state(struct wd_state *state, bool manual) {
+  state->apply_manual = state->apply_manual || manual;
   gtk_stack_set_visible_child_name(GTK_STACK(state->header_stack), "title");
   if (!state->autoapply) {
     gtk_style_context_add_class(gtk_widget_get_style_context(state->spinner), "visible");
@@ -300,7 +302,7 @@ static void show_apply(struct wd_state *state) {
   const gchar *page = "title";
   if (has_changes(state)) {
     if (state->autoapply) {
-      apply_state(state);
+      apply_state(state, false);
     } else {
       page = "apply";
     }
@@ -842,7 +844,7 @@ static void cancel_changes(GSimpleAction *action, GVariant *param, gpointer data
 }
 
 static void apply_changes(GSimpleAction *action, GVariant *param, gpointer data) {
-  apply_state(data);
+  apply_state(data, true);
 }
 
 static void info_response(GtkInfoBar *info_bar, gint response_id, gpointer data) {
diff --git a/src/outputs.c b/src/outputs.c
index f41ee01..6cec53a 100644
--- a/src/outputs.c
+++ b/src/outputs.c
@@ -35,6 +35,7 @@ static void noop() {
 struct wd_pending_config {
   struct wd_state *state;
   struct wl_list *outputs;
+  bool manual;
 };
 
 static void destroy_pending(struct wd_pending_config *pending) {
@@ -53,7 +54,7 @@ static void config_handle_succeeded(void *data,
   zwlr_output_configuration_v1_destroy(config);
   wd_ui_apply_done(pending->state, pending->outputs);
 #ifdef WITH_KANSHI
-  if (pending->state->save_kanshi_config) {
+  if (pending->manual && pending->state->save_kanshi_config) {
     wd_store_config(pending->state, pending->outputs);
   }
 #endif
@@ -95,6 +96,7 @@ void wd_apply_state(struct wd_state *state, struct wl_list *new_outputs,
   struct wd_pending_config *pending = calloc(1, sizeof(*pending));
   pending->state = state;
   pending->outputs = new_outputs;
+  pending->manual = state->apply_manual;
 
   zwlr_output_configuration_v1_add_listener(config, &config_listener, pending);
 
diff --git a/src/wdisplays.h b/src/wdisplays.h
index 83690a2..dbdb03d 100644
--- a/src/wdisplays.h
+++ b/src/wdisplays.h
@@ -187,6 +187,7 @@ struct wd_state {
   uint32_t serial;
 
   bool apply_pending;
+  bool apply_manual;
   bool autoapply;
   bool capture;
   bool show_overlay;