diff --git a/CMakeLists.txt b/CMakeLists.txt
index a6e879447..e3feeed43 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -161,8 +161,8 @@ endif()
 
 
 # Write binaries to a seperate directory.
-if(WIN32)
-  # For Windows, use the source directory.
+if(WIN32 AND NOT BUILD_LIBRETRO_CORE)
+  # For Windows, use the source directory, except for libretro.
   set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin/${CPU_ARCH}")
 else()
   set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/bin")