diff --git a/sway/commands/output.c b/sway/commands/output.c
index 11da0ff6..be78358a 100644
--- a/sway/commands/output.c
+++ b/sway/commands/output.c
@@ -227,7 +227,7 @@ struct cmd_results *cmd_output(int argc, char **argv) {
 	if (output->name) {
 		// Try to find the output container and apply configuration now. If
 		// this is during startup then there will be no container and config
-		// will be applied during normal "new output" event from wlc.
+		// will be applied during normal "new output" event from wlroots.
 		swayc_t *cont = NULL;
 		for (int i = 0; i < root_container.children->length; ++i) {
 			cont = root_container.children->items[i];
diff --git a/sway/config/output.c b/sway/config/output.c
index 26798503..027a79ce 100644
--- a/sway/config/output.c
+++ b/sway/config/output.c
@@ -91,12 +91,13 @@ static void set_mode(struct wlr_output *output, int width, int height,
 void apply_output_config(struct output_config *oc, swayc_t *output) {
 	assert(output->type == C_OUTPUT);
 
+	struct wlr_output *wlr_output = output->sway_output->wlr_output;
 	if (oc && oc->enabled == 0) {
+		wlr_output_layout_remove(root_container.output_layout, wlr_output);
 		destroy_output(output);
 		return;
 	}
 
-	struct wlr_output *wlr_output = output->sway_output->wlr_output;
 	if (oc && oc->width > 0 && oc->height > 0) {
 		set_mode(wlr_output, oc->width, oc->height, oc->refresh_rate);
 	}
diff --git a/sway/tree/container.c b/sway/tree/container.c
index d9bed7d8..e4c27d61 100644
--- a/sway/tree/container.c
+++ b/sway/tree/container.c
@@ -8,6 +8,7 @@
 #include "sway/container.h"
 #include "sway/layout.h"
 #include "sway/output.h"
+#include "sway/server.h"
 #include "sway/view.h"
 #include "sway/workspace.h"
 #include "log.h"
@@ -172,6 +173,7 @@ swayc_t *destroy_output(swayc_t *output) {
 	if (!sway_assert(output, "null output passed to destroy_output")) {
 		return NULL;
 	}
+
 	if (output->children->length > 0) {
 		// TODO save workspaces when there are no outputs.
 		// TODO also check if there will ever be no outputs except for exiting
@@ -190,9 +192,11 @@ swayc_t *destroy_output(swayc_t *output) {
 			arrange_windows(root_container.children->items[p], -1, -1);
 		}
 	}
+
 	sway_log(L_DEBUG, "OUTPUT: Destroying output '%s'", output->name);
 	free_swayc(output);
 	update_root_geometry();
+
 	return &root_container;
 }