diff --git a/sway/commands/input.c b/sway/commands/input.c
index 35846b1c..310375a9 100644
--- a/sway/commands/input.c
+++ b/sway/commands/input.c
@@ -94,7 +94,7 @@ struct cmd_results *cmd_input(int argc, char **argv) {
 			return res;
 		}
 
-		if (!config->reloading) {
+		if (!config->reading) {
 			input_manager_apply_input_config(ic);
 		}
 	} else {
diff --git a/sway/commands/output.c b/sway/commands/output.c
index 3f65b909..9d58413f 100644
--- a/sway/commands/output.c
+++ b/sway/commands/output.c
@@ -107,17 +107,16 @@ struct cmd_results *cmd_output(int argc, char **argv) {
 
 	store_output_config(output);
 
-	// If reloading, the output configs will be applied after reading the
-	// entire config and before the deferred commands so that an auto generated
-	// workspace name is not given to re-enabled outputs.
-	if (!config->reloading && !config->validating) {
-		apply_stored_output_configs();
-		if (background) {
-			if (!spawn_swaybg()) {
-				return cmd_results_new(CMD_FAILURE,
-					"Failed to apply background configuration");
-			}
-		}
+	if (config->reading) {
+		// When reading the config file, we wait till the end to do a single
+		// modeset and swaybg spawn.
+		return cmd_results_new(CMD_SUCCESS, NULL);
+	}
+	request_modeset();
+
+	if (background && !spawn_swaybg()) {
+		return cmd_results_new(CMD_FAILURE,
+			"Failed to apply background configuration");
 	}
 
 	return cmd_results_new(CMD_SUCCESS, NULL);
diff --git a/sway/config.c b/sway/config.c
index 5fc414a1..1090edc5 100644
--- a/sway/config.c
+++ b/sway/config.c
@@ -516,7 +516,7 @@ bool load_main_config(const char *file, bool is_active, bool validating) {
 	// Only really necessary if not explicitly `font` is set in the config.
 	config_update_font_height();
 
-	if (is_active && !validating) {
+	if (!validating) {
 		input_manager_verify_fallback_seat();
 
 		for (int i = 0; i < config->input_configs->length; i++) {
@@ -533,12 +533,14 @@ bool load_main_config(const char *file, bool is_active, bool validating) {
 		}
 		sway_switch_retrigger_bindings_for_all();
 
-		apply_stored_output_configs();
 		spawn_swaybg();
 
 		config->reloading = false;
-		if (config->swaynag_config_errors.client != NULL) {
-			swaynag_show(&config->swaynag_config_errors);
+		if (is_active) {
+			request_modeset();
+			if (config->swaynag_config_errors.client != NULL) {
+				swaynag_show(&config->swaynag_config_errors);
+			}
 		}
 	}