diff --git a/pcsx2/VU0micro.cpp b/pcsx2/VU0micro.cpp
index 651ed8102d..3be6664d0b 100644
--- a/pcsx2/VU0micro.cpp
+++ b/pcsx2/VU0micro.cpp
@@ -42,6 +42,8 @@ void __fastcall vu0ExecMicro(u32 addr) {
 		vu0Finish();
 	}
 
+	// Need to copy the clip flag back to the interpreter in case COP2 has edited it
+	VU0.clipflag = VU0.VI[REG_CLIP_FLAG].UL;
 	VU0.VI[REG_VPU_STAT].UL &= ~0xFF;
 	VU0.VI[REG_VPU_STAT].UL |=  0x01;
 	VU0.cycle = cpuRegs.cycle;
diff --git a/pcsx2/x86/microVU_Alloc.inl b/pcsx2/x86/microVU_Alloc.inl
index 2c8a9d799d..fa65645b61 100644
--- a/pcsx2/x86/microVU_Alloc.inl
+++ b/pcsx2/x86/microVU_Alloc.inl
@@ -109,6 +109,14 @@ __fi void mVUallocCFLAGb(mV, const x32& reg, int fInstance)
 {
 	if (fInstance < 4) xMOV(ptr32[&mVU.clipFlag[fInstance]], reg);			// microVU
 	else			   xMOV(ptr32[&mVU.regs().VI[REG_CLIP_FLAG].UL], reg);	// macroVU
+
+	// On COP2 modifying the CLIP flag we need to update the microVU version for when it's restored on new program
+	if (fInstance == 0xff)
+	{
+		xMOVDZX(xmmT1, reg);
+		xSHUF.PS(xmmT1, xmmT1, 0);
+		xMOVAPS(ptr128[&mVU.regs().micro_clipflags], xmmT1);
+	}
 }
 
 //------------------------------------------------------------------