diff --git a/src/main.c b/src/main.c
index 86052cb..fc89247 100644
--- a/src/main.c
+++ b/src/main.c
@@ -426,7 +426,7 @@ static void cleanup(GtkWidget *window, gpointer data) {
   g_object_unref(state->move_cursor);
   g_clear_object(&state->settings);
 #ifdef WITH_KANSHI
-  wd_store_config_if_dirty(state);
+  wd_save_kanshi_snapshot(state);
 #endif
   wd_state_destroy(state);
 }
@@ -875,7 +875,7 @@ static void auto_apply_selected(GSimpleAction *action, GVariant *param, gpointer
   g_simple_action_set_state(action, param);
 #ifdef WITH_KANSHI
   if (!state->autoapply) {
-    wd_store_config_if_dirty(state);
+    wd_save_kanshi_snapshot(state);
   }
 #endif
 }
@@ -925,7 +925,7 @@ static void save_kanshi_config_selected(GSimpleAction *action, GVariant *param,
     g_settings_set_boolean(state->settings, "save-kanshi-config", g_variant_get_boolean(param));
   }
   state->save_kanshi_config = g_variant_get_boolean(param);
-  state->kanshi_dirty = false;
+  wd_drop_kanshi_snapshot(state);
   g_simple_action_set_state(action, param);
 }
 #endif
diff --git a/src/outputs.c b/src/outputs.c
index 9d0ce60..8d5662f 100644
--- a/src/outputs.c
+++ b/src/outputs.c
@@ -38,16 +38,38 @@ struct wd_pending_config {
   bool manual;
 };
 
-static void destroy_pending(struct wd_pending_config *pending) {
+static void destroy_outputs(struct wl_list *outputs) {
   struct wd_head_config *output, *tmp;
-  wl_list_for_each_safe(output, tmp, pending->outputs, link) {
+  wl_list_for_each_safe(output, tmp, outputs, link) {
     wl_list_remove(&output->link);
     free(output);
   }
-  free(pending->outputs);
+  free(outputs);
+}
+
+static void destroy_pending(struct wd_pending_config *pending) {
+  if (pending->outputs != NULL) {
+    destroy_outputs(pending->outputs);
+  }
   free(pending);
 }
 
+#ifdef WITH_KANSHI
+void wd_drop_kanshi_snapshot(struct wd_state *state) {
+  if (state->kanshi_snapshot != NULL) {
+    destroy_outputs(state->kanshi_snapshot);
+    state->kanshi_snapshot = NULL;
+  }
+}
+
+void wd_save_kanshi_snapshot(struct wd_state *state) {
+  if (state->kanshi_snapshot != NULL) {
+    wd_store_config(state, state->kanshi_snapshot);
+    wd_drop_kanshi_snapshot(state);
+  }
+}
+#endif
+
 static void config_handle_succeeded(void *data,
     struct zwlr_output_configuration_v1 *config) {
   struct wd_pending_config *pending = data;
@@ -55,10 +77,13 @@ static void config_handle_succeeded(void *data,
   wd_ui_apply_done(pending->state, pending->outputs);
 #ifdef WITH_KANSHI
   if (pending->state->save_kanshi_config) {
+    wd_drop_kanshi_snapshot(pending->state);
     if (pending->manual) {
       wd_store_config(pending->state, pending->outputs);
+    } else {
+      pending->state->kanshi_snapshot = pending->outputs;
+      pending->outputs = NULL;
     }
-    pending->state->kanshi_dirty = !pending->manual;
   }
 #endif
   destroy_pending(pending);
@@ -491,6 +516,9 @@ static void head_handle_finished(void *data,
     struct zwlr_output_head_v1 *wlr_head) {
   struct wd_head *head = data;
   struct wd_state *state = head->state;
+#ifdef WITH_KANSHI
+  wd_save_kanshi_snapshot(state);
+#endif
   wl_list_remove(&head->link);
   wd_head_destroy(head);
 
@@ -526,6 +554,9 @@ static void output_manager_handle_head(void *data,
     struct zwlr_output_manager_v1 *manager,
     struct zwlr_output_head_v1 *wlr_head) {
   struct wd_state *state = data;
+#ifdef WITH_KANSHI
+  wd_save_kanshi_snapshot(state);
+#endif
 
   struct wd_head *head = calloc(1, sizeof(*head));
   head->state = state;
diff --git a/src/store.c b/src/store.c
index 8b9fe8a..4e6a166 100644
--- a/src/store.c
+++ b/src/store.c
@@ -634,37 +634,6 @@ static void reload_kanshi(void) {
   }
 }
 
-void wd_store_config_if_dirty(struct wd_state *state) {
-  if (!state->kanshi_dirty) {
-    return;
-  }
-  state->kanshi_dirty = false;
-
-  struct wl_list outputs;
-  wl_list_init(&outputs);
-  struct wd_head *head;
-  wl_list_for_each(head, &state->heads, link) {
-    struct wd_head_config *output = g_new0(struct wd_head_config, 1);
-    output->head = head;
-    output->enabled = head->enabled;
-    output->width = head->mode != NULL ? head->mode->width : head->custom_mode.width;
-    output->height = head->mode != NULL ? head->mode->height : head->custom_mode.height;
-    output->refresh = head->mode != NULL ? head->mode->refresh : head->custom_mode.refresh;
-    output->x = head->x;
-    output->y = head->y;
-    output->scale = head->scale;
-    output->transform = head->transform;
-    wl_list_insert(&outputs, &output->link);
-  }
-  wd_store_config(state, &outputs);
-
-  struct wd_head_config *output, *tmp;
-  wl_list_for_each_safe(output, tmp, &outputs, link) {
-    wl_list_remove(&output->link);
-    g_free(output);
-  }
-}
-
 void wd_store_config(struct wd_state *state, struct wl_list *outputs) {
   g_autofree char *path = get_config_path();
   g_autoptr(GPtrArray) files = g_ptr_array_new_with_free_func(kanshi_file_free);
diff --git a/src/wdisplays.h b/src/wdisplays.h
index ffec9bf..90f039f 100644
--- a/src/wdisplays.h
+++ b/src/wdisplays.h
@@ -192,7 +192,7 @@ struct wd_state {
   bool capture;
   bool show_overlay;
   bool save_kanshi_config;
-  bool kanshi_dirty;
+  struct wl_list *kanshi_snapshot;
   double zoom;
 
   unsigned int apply_idle;
@@ -355,10 +355,15 @@ void wd_destroy_overlay(struct wd_output *output);
 void wd_store_config(struct wd_state *state, struct wl_list *outputs);
 
 /*
- * Saves the current layout to the kanshi config if auto-apply changed it
- * since the last save.
+ * Saves the layout of the last auto-apply to the kanshi config, unless it
+ * has been saved or dropped already.
  */
-void wd_store_config_if_dirty(struct wd_state *state);
+void wd_save_kanshi_snapshot(struct wd_state *state);
+
+/*
+ * Forgets the layout of the last auto-apply without saving it.
+ */
+void wd_drop_kanshi_snapshot(struct wd_state *state);
 #endif
 // SPDX-SnippetEnd
 #endif