diff --git a/pcsx2/CMakeLists.txt b/pcsx2/CMakeLists.txt
index 4829ee8971..a2de0bb001 100644
--- a/pcsx2/CMakeLists.txt
+++ b/pcsx2/CMakeLists.txt
@@ -1495,6 +1495,10 @@ set(pcsx2LTOSources
 	${pcsx2IPUHeaders}
 	${pcsx2x86Sources}
 	${pcsx2x86Headers}
+	${pcsx2SPU2Sources}
+	${pcsx2SPU2Headers}
+	${pcsx2GSSources}
+	${pcsx2GSHeaders}
 )
 
 if(LTO_PCSX2_CORE)
@@ -1502,6 +1506,7 @@ if(LTO_PCSX2_CORE)
 	target_link_libraries(PCSX2_LTO PRIVATE PCSX2_FLAGS)
 	target_link_libraries(PCSX2 PRIVATE PCSX2_LTO)
 	set_target_properties(PCSX2_LTO PROPERTIES INTERPROCEDURAL_OPTIMIZATION true)
+	fixup_file_properties(PCSX2_LTO)
 else()
 	target_sources(PCSX2 PRIVATE ${pcsx2LTOSources})
 endif()
@@ -1510,14 +1515,10 @@ endif()
 target_sources(PCSX2 PRIVATE
 	${pcsx2CDVDSources}
 	${pcsx2CDVDHeaders}
-	${pcsx2SPU2Sources}
-	${pcsx2SPU2Headers}
 	${pcsx2DEV9Sources}
 	${pcsx2DEV9Headers}
 	${pcsx2PADHeaders}
 	${pcsx2PADSources}
-	${pcsx2GSHeaders}
-	${pcsx2GSSources}
 	${pcsx2RecordingSources}
 	${pcsx2DebugToolsSources}
 	${pcsx2DebugToolsHeaders}