diff --git a/pcsx2-qt/EmuThread.cpp b/pcsx2-qt/EmuThread.cpp
index a2f7fea0bf..43247b6e4b 100644
--- a/pcsx2-qt/EmuThread.cpp
+++ b/pcsx2-qt/EmuThread.cpp
@@ -114,7 +114,18 @@ void EmuThread::startVM(std::shared_ptr<VMBootParameters> boot_params)
 	if (!VMManager::Initialize(*boot_params))
 		return;
 
-	VMManager::SetState(VMState::Running);
+	if (!Host::GetBoolSettingValue("UI", "StartPaused", false))
+	{
+		// This will come back and call OnVMResumed().
+		VMManager::SetState(VMState::Running);
+	}
+	else
+	{
+		// When starting paused, redraw the window, so there's at least something there.
+		redrawDisplayWindow();
+		Host::OnVMPaused();
+	}
+
 	m_event_loop->quit();
 }
 
@@ -609,6 +620,21 @@ void EmuThread::onDisplayWindowResized(int width, int height, float scale)
 
 void EmuThread::onDisplayWindowFocused() {}
 
+void EmuThread::redrawDisplayWindow()
+{
+	if (!isOnEmuThread())
+	{
+		QMetaObject::invokeMethod(this, &EmuThread::redrawDisplayWindow, Qt::QueuedConnection);
+		return;
+	}
+
+	// If we're running, we're going to re-present anyway.
+	if (!VMManager::HasValidVM() || VMManager::GetState() == VMState::Running)
+		return;
+
+	GetMTGS().RunOnGSThread([]() { GetMTGS().PresentCurrentFrame(); });
+}
+
 void EmuThread::runOnCPUThread(const std::function<void()>& func)
 {
 	func();
diff --git a/pcsx2-qt/EmuThread.h b/pcsx2-qt/EmuThread.h
index cefdb2a2b8..bd0ee0dcd1 100644
--- a/pcsx2-qt/EmuThread.h
+++ b/pcsx2-qt/EmuThread.h
@@ -146,6 +146,7 @@ private Q_SLOTS:
 	void doBackgroundControllerPoll();
 	void onDisplayWindowResized(int width, int height, float scale);
 	void onDisplayWindowFocused();
+	void redrawDisplayWindow();
 
 private:
 	QThread* m_ui_thread;
diff --git a/pcsx2-qt/Settings/InterfaceSettingsWidget.cpp b/pcsx2-qt/Settings/InterfaceSettingsWidget.cpp
index cdb15182a6..b78b14c5d2 100644
--- a/pcsx2-qt/Settings/InterfaceSettingsWidget.cpp
+++ b/pcsx2-qt/Settings/InterfaceSettingsWidget.cpp
@@ -117,7 +117,6 @@ InterfaceSettingsWidget::InterfaceSettingsWidget(SettingsDialog* dialog, QWidget
 		tr("Hides the main window (with the game list) when a game is running, requires Render To Separate Window to be enabled."));
 
 	// Not yet used, disable the options
-	m_ui.pauseOnStart->setDisabled(true);
 	m_ui.pauseOnFocusLoss->setDisabled(true);
 	m_ui.language->setDisabled(true);
 
diff --git a/pcsx2/Frontend/ImGuiManager.cpp b/pcsx2/Frontend/ImGuiManager.cpp
index 50c7d6d268..b58fcbeb90 100644
--- a/pcsx2/Frontend/ImGuiManager.cpp
+++ b/pcsx2/Frontend/ImGuiManager.cpp
@@ -27,6 +27,10 @@
 #include "common/Timer.h"
 #include "imgui.h"
 
+#ifdef PCSX2_CORE
+#include "imgui_internal.h"
+#endif
+
 #include "Config.h"
 #include "Counters.h"
 #include "Frontend/ImGuiManager.h"
@@ -198,6 +202,9 @@ void ImGuiManager::NewFrame()
 	ImGui::NewFrame();
 
 #ifdef PCSX2_CORE
+	// Disable nav input on the implicit (Debug##Default) window. Otherwise we end up requesting keyboard
+	// focus when there's nothing there. We use GetCurrentWindowRead() because otherwise it'll make it visible.
+	ImGui::GetCurrentWindowRead()->Flags |= ImGuiWindowFlags_NoNavInputs;
 	s_imgui_wants_keyboard.store(io.WantCaptureKeyboard, std::memory_order_relaxed);
 	s_imgui_wants_mouse.store(io.WantCaptureMouse, std::memory_order_release);
 #endif