diff --git a/sway/commands/seat.c b/sway/commands/seat.c
index 3e7ffed9d..b8db862b1 100644
--- a/sway/commands/seat.c
+++ b/sway/commands/seat.c
@@ -35,7 +35,9 @@ struct cmd_results *cmd_seat(int argc, char **argv) {
 
 	struct seat_config *sc =
 		store_seat_config(config->handler_context.seat_config);
-	input_manager_apply_seat_config(sc);
+	if (!config->reading) {
+		input_manager_apply_seat_config(sc);
+	}
 
 	config->handler_context.seat_config = NULL;
 	return cmd_results_new(CMD_SUCCESS, NULL, NULL);
diff --git a/sway/config.c b/sway/config.c
index 8a0b293c6..dfbe4cb96 100644
--- a/sway/config.c
+++ b/sway/config.c
@@ -463,7 +463,11 @@ bool load_main_config(const char *file, bool is_active, bool validating) {
 		if (config->swaynag_config_errors.pid > 0) {
 			swaynag_show(&config->swaynag_config_errors);
 		}
+
 		input_manager_verify_fallback_seat();
+		for (int i = 0; i < config->seat_configs->length; i++) {
+			input_manager_apply_seat_config(config->seat_configs->items[i]);
+		}
 	}
 
 	if (old_config) {