diff --git a/Core/Config.cpp b/Core/Config.cpp
index aa62b14d08..a0d7e7107b 100644
--- a/Core/Config.cpp
+++ b/Core/Config.cpp
@@ -53,6 +53,7 @@
 #include "Core/ConfigValues.h"
 #include "Core/Loaders.h"
 #include "Core/KeyMap.h"
+#include "Core/System.h"
 #include "Core/HLE/sceUtility.h"
 #include "Core/Instance.h"
 #include "GPU/Common/FramebufferManagerCommon.h"
@@ -1679,7 +1680,9 @@ const Path Config::FindConfigFile(const std::string &baseFilename) {
 	Path parent = filename.NavigateUp();
 
 	// We try to create the path and ignore if it fails (already exists).
-	File::CreateFullPath(parent);
+	if (parent != GetSysDirectory(DIRECTORY_SYSTEM)) {
+		File::CreateFullPath(parent);
+	}
 	return filename;
 }
 
diff --git a/Windows/main.cpp b/Windows/main.cpp
index 50b20cd3a2..2092900862 100644
--- a/Windows/main.cpp
+++ b/Windows/main.cpp
@@ -838,10 +838,8 @@ static void InitMemstickDirectory() {
 	// We're screwed anyway if we can't write to Documents, or can't detect it.
 	if (!File::CreateEmptyFile(testFile))
 		g_Config.memStickDirectory = myDocsPath;
-
 	// Clean up our mess.
-	if (File::Exists(testFile))
-		File::Delete(testFile);
+	File::Delete(testFile);
 }
 
 static void WinMainInit() {