diff --git a/CMakeModules/DuckStationUtils.cmake b/CMakeModules/DuckStationUtils.cmake
index 12d7a52ed..9758f14fb 100644
--- a/CMakeModules/DuckStationUtils.cmake
+++ b/CMakeModules/DuckStationUtils.cmake
@@ -69,8 +69,10 @@ function(detect_architecture)
          CMAKE_SIZEOF_VOID_P EQUAL 8)
     message(STATUS "Building x86_64 binaries.")
     set(CPU_ARCH_X64 TRUE PARENT_SCOPE)
-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -msse4.1" PARENT_SCOPE)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4.1" PARENT_SCOPE)
+    if(NOT MSVC OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+      set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -msse4.1" PARENT_SCOPE)
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4.1" PARENT_SCOPE)
+    endif()
   elseif(("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "aarch64" OR "${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "arm64") AND
          CMAKE_SIZEOF_VOID_P EQUAL 8) # Might have an A64 kernel, e.g. Raspbian.
     message(STATUS "Building ARM64 binaries.")