diff --git a/pcsx2/VMManager.cpp b/pcsx2/VMManager.cpp
index 0835966c44..ab815b7bed 100644
--- a/pcsx2/VMManager.cpp
+++ b/pcsx2/VMManager.cpp
@@ -681,7 +681,12 @@ void VMManager::UpdateRunningGame(bool resetting, bool game_starting)
 	UpdateGameSettingsLayer();
 	ApplySettings();
 
-	// check this here, for two cases: dynarec on, and when enable cheats is set per-game.
+	// Clear the memory card eject notification again when booting for the first time, or starting.
+	// Otherwise, games think the card was removed on boot.
+	if (game_starting || resetting)
+		ClearMcdEjectTimeoutNow();
+
+	// Check this here, for two cases: dynarec on, and when enable cheats is set per-game.
 	if (s_patches_crc != s_game_crc)
 		ReloadPatches(game_starting, false);