diff --git a/pcsx2-qt/Settings/SystemSettingsWidget.cpp b/pcsx2-qt/Settings/SystemSettingsWidget.cpp
index 2c2ce7609b..93150fa208 100644
--- a/pcsx2-qt/Settings/SystemSettingsWidget.cpp
+++ b/pcsx2-qt/Settings/SystemSettingsWidget.cpp
@@ -94,18 +94,10 @@ SystemSettingsWidget::SystemSettingsWidget(SettingsDialog* dialog, QWidget* pare
 
 	dialog->registerWidgetHelp(m_ui.fastCDVD, tr("Enable Fast CDVD"), tr("Unchecked"),
 		tr("Fast disc access, less loading times. Check HDLoader compatibility lists for known games that have issues with this."));
-
-	updateVU1InstantState();
-	connect(m_ui.MTVU, &QCheckBox::stateChanged, this, &SystemSettingsWidget::updateVU1InstantState);
 }
 
 SystemSettingsWidget::~SystemSettingsWidget() = default;
 
-void SystemSettingsWidget::updateVU1InstantState()
-{
-	//m_ui.instantVU1->setEnabled(!m_dialog->getEffectiveBoolValue("EmuCore/Speedhacks", "vuThread", false));
-}
-
 int SystemSettingsWidget::getGlobalClampingModeIndex(bool vu) const
 {
 	if (Host::GetBaseBoolSettingValue("EmuCore/CPU/Recompiler", vu ? "vuSignOverflow" : "fpuFullMode", false))
diff --git a/pcsx2-qt/Settings/SystemSettingsWidget.h b/pcsx2-qt/Settings/SystemSettingsWidget.h
index 6b760b1b78..2e5a7a97cf 100644
--- a/pcsx2-qt/Settings/SystemSettingsWidget.h
+++ b/pcsx2-qt/Settings/SystemSettingsWidget.h
@@ -29,9 +29,6 @@ public:
 	SystemSettingsWidget(SettingsDialog* dialog, QWidget* parent);
 	~SystemSettingsWidget();
 
-private Q_SLOTS:
-	void updateVU1InstantState();
-
 private:
 	int getGlobalClampingModeIndex(bool vu) const;
 	int getClampingModeIndex(bool vu) const;
diff --git a/pcsx2/MTVU.cpp b/pcsx2/MTVU.cpp
index a058f95502..0702901379 100644
--- a/pcsx2/MTVU.cpp
+++ b/pcsx2/MTVU.cpp
@@ -416,7 +416,7 @@ void VU_Thread::Get_MTVUChanges()
 	{
 		mtvuInterrupts.fetch_and(~InterruptFlagVUEBit, std::memory_order_relaxed);
 		
-		if(!INSTANT_VU1)
+		if(INSTANT_VU1)
 			VU0.VI[REG_VPU_STAT].UL &= ~0xFF00;
 		//DevCon.Warning("E-Bit registered %x", VU0.VI[REG_VPU_STAT].UL);
 	}
diff --git a/pcsx2/R5900.cpp b/pcsx2/R5900.cpp
index 7a6692fff3..a43cfb9c29 100644
--- a/pcsx2/R5900.cpp
+++ b/pcsx2/R5900.cpp
@@ -528,7 +528,7 @@ __fi void CPU_INT( EE_EventType n, s32 ecycle)
 	// EE events happen 8 cycles in the future instead of whatever was requested.
 	// This can be used on games with PATH3 masking issues for example, or when
 	// some FMV look bad.
-	if(CHECK_EETIMINGHACK) ecycle = 8;
+	if(CHECK_EETIMINGHACK && n < VIF_VU0_FINISH) ecycle = 8;
 
 	cpuRegs.interrupt|= 1 << n;
 	cpuRegs.sCycle[n] = cpuRegs.cycle;
diff --git a/pcsx2/VU1micro.cpp b/pcsx2/VU1micro.cpp
index 5f429fab20..32d7d0ffd2 100644
--- a/pcsx2/VU1micro.cpp
+++ b/pcsx2/VU1micro.cpp
@@ -38,7 +38,10 @@ void vu1ResetRegs()
 void vu1Finish(bool add_cycles) {
 	if (THREAD_VU1) {
 		//if (VU0.VI[REG_VPU_STAT].UL & 0x100) DevCon.Error("MTVU: VU0.VI[REG_VPU_STAT].UL & 0x100");
-		vu1Thread.WaitVU();
+		if (INSTANT_VU1 || add_cycles)
+		{
+			vu1Thread.WaitVU();
+		}
 		vu1Thread.Get_MTVUChanges();
 		return;
 	}
diff --git a/pcsx2/Vif1_Dma.cpp b/pcsx2/Vif1_Dma.cpp
index ef98d45e00..e93a88a9bd 100644
--- a/pcsx2/Vif1_Dma.cpp
+++ b/pcsx2/Vif1_Dma.cpp
@@ -228,8 +228,11 @@ __fi void vif1VUFinish()
 	if (VU0.VI[REG_VPU_STAT].UL & 0x500)
 	{
 		vu1Thread.Get_MTVUChanges();
-
-		CPU_INT(VIF_VU1_FINISH, 128);
+		
+		if (THREAD_VU1 && !INSTANT_VU1 && (VU0.VI[REG_VPU_STAT].UL & 0x100))
+			CPU_INT(VIF_VU1_FINISH, cpuGetCycles(VU_MTVU_BUSY));
+		else
+			CPU_INT(VIF_VU1_FINISH, 128);
 		return;
 	}
 	
diff --git a/pcsx2/gui/Panels/ConfigurationPanels.h b/pcsx2/gui/Panels/ConfigurationPanels.h
index 2cee6b985c..41007448ee 100644
--- a/pcsx2/gui/Panels/ConfigurationPanels.h
+++ b/pcsx2/gui/Panels/ConfigurationPanels.h
@@ -341,7 +341,6 @@ namespace Panels
 		void Defaults_Click(wxCommandEvent& evt);
 		void EECycleRate_Scroll(wxScrollEvent& event);
 		void VUCycleRate_Scroll(wxScrollEvent& event);
-		void VUThread_Enable(wxCommandEvent& evt);
 	};
 
 	// --------------------------------------------------------------------------------------
diff --git a/pcsx2/gui/Panels/SpeedhacksPanel.cpp b/pcsx2/gui/Panels/SpeedhacksPanel.cpp
index 4b0298fcda..c1d7fae214 100644
--- a/pcsx2/gui/Panels/SpeedhacksPanel.cpp
+++ b/pcsx2/gui/Panels/SpeedhacksPanel.cpp
@@ -173,7 +173,7 @@ Panels::SpeedHacksPanel::SpeedHacksPanel( wxWindow* parent )
 	m_check_vuFlagHack->SetToolTip( pxEt( L"Updates Status Flags only on blocks which will read them, instead of all the time. This is safe most of the time."
 	) );
 
-	m_check_vuThread->SetToolTip( pxEt( L"Runs VU1 on its own thread (microVU1-only). Generally a speedup on CPUs with 3 or more cores. This is safe for most games, but a few games are incompatible and may hang. In the case of GS limited games, it may be a slowdown (especially on dual core CPUs)."
+	m_check_vuThread->SetToolTip( pxEt( L"Runs VU1 on its own thread. Generally a speedup on CPUs with 3 or more cores. This is safe for most games, but a few games are incompatible and may hang. In the case of GS limited games, it may be a slowdown (especially on dual core CPUs)."
 	) );
 
 	m_check_vu1Instant->SetToolTip(pxEt(L"Runs VU1 instantly. Provides a modest speed improvement in most games. This is safe for most games, but a few games may exhibit graphical errors."
@@ -237,7 +237,6 @@ Panels::SpeedHacksPanel::SpeedHacksPanel( wxWindow* parent )
 	Bind(wxEVT_SCROLL_CHANGED, &SpeedHacksPanel::VUCycleRate_Scroll, this, m_slider_eeSkip->GetId());
 	Bind(wxEVT_CHECKBOX, &SpeedHacksPanel::OnEnable_Toggled, this, m_check_Enable->GetId());
 	Bind(wxEVT_BUTTON, &SpeedHacksPanel::Defaults_Click, this, wxID_DEFAULT);
-	Bind(wxEVT_CHECKBOX, &SpeedHacksPanel::VUThread_Enable, this, m_check_vuThread->GetId());
 }
 
 // Doesn't modify values - only locks(gray out)/unlocks as necessary.
@@ -267,11 +266,6 @@ void Panels::SpeedHacksPanel::EnableStuff( AppConfig* configToUse )
 	// Grayout MTVU on safest preset
 	m_check_vuThread->Enable(hacksEnabled && (!hasPreset || configToUse->PresetIndex != 0));
 
-	// Disables the Instant VU1 checkbox when MTVU is checked in the GUI as reflected in the code.
-	// Makes Instant VU1 toggleable when MTVU is unchecked in the GUI.
-	// Some may think that having MTVU + Instant VU1 checked, can have bad side-effects when it doesn't.
-	//m_check_vu1Instant->Enable(hacksEnabled && !m_check_vuThread->GetValue());
-
 	// Layout necessary to ensure changed slider text gets re-aligned properly
 	// and to properly gray/ungray pxStaticText stuff (I suspect it causes a
 	// paint event to be sent on Windows)
@@ -370,9 +364,3 @@ void Panels::SpeedHacksPanel::VUCycleRate_Scroll(wxScrollEvent &event)
 
 	event.Skip();
 }
-
-void Panels::SpeedHacksPanel::VUThread_Enable(wxCommandEvent& evt)
-{
-	m_check_vu1Instant->Enable(!m_check_vuThread->GetValue());
-	Layout();
-}