diff --git a/rpcs3/Emu/CPU/CPUThread.cpp b/rpcs3/Emu/CPU/CPUThread.cpp
index 9fdc8d92bd..806bd7e54c 100644
--- a/rpcs3/Emu/CPU/CPUThread.cpp
+++ b/rpcs3/Emu/CPU/CPUThread.cpp
@@ -1023,6 +1023,44 @@ cpu_thread& cpu_thread::operator=(thread_state)
 	return *this;
 }
 
+void cpu_thread::add_remove_flags(bs_t<cpu_flag> to_add, bs_t<cpu_flag> to_remove)
+{
+	bs_t<cpu_flag> result{};
+
+	if (!to_remove)
+	{
+		state.add_fetch(to_add);
+		return;
+	}
+	else if (!to_add)
+	{
+		result = state.sub_fetch(to_remove);
+	}
+	else
+	{
+		result = state.atomic_op([&](bs_t<cpu_flag>& v)
+		{
+			v += to_add;
+			v -= to_remove;
+			return v;
+		});
+	}
+
+	if (!::is_paused(to_remove) && !::is_stopped(to_remove))
+	{
+		// No notable change requiring notification
+		return;
+	}
+
+	if (::is_paused(result) || ::is_stopped(result))
+	{
+		// Flags that stop thread execution
+		return;
+	}
+
+	state.notify_one();
+}
+
 std::string cpu_thread::get_name() const
 {
 	// Downcast to correct type
diff --git a/rpcs3/Emu/CPU/CPUThread.h b/rpcs3/Emu/CPU/CPUThread.h
index cfdee6db4b..a11e4cd869 100644
--- a/rpcs3/Emu/CPU/CPUThread.h
+++ b/rpcs3/Emu/CPU/CPUThread.h
@@ -149,7 +149,9 @@ public:
 	void notify();
 	cpu_thread& operator=(thread_state);
 
-public:
+	// Add/remove CPU state flags in an atomic operations, notifying if required
+	void add_remove_flags(bs_t<cpu_flag> to_add, bs_t<cpu_flag> to_remove);
+
 	// Thread stats for external observation
 	static atomic_t<u64> g_threads_created, g_threads_deleted, g_suspend_counter;
 
diff --git a/rpcs3/Emu/RSX/RSXThread.cpp b/rpcs3/Emu/RSX/RSXThread.cpp
index 244ad670b1..892ce75a34 100644
--- a/rpcs3/Emu/RSX/RSXThread.cpp
+++ b/rpcs3/Emu/RSX/RSXThread.cpp
@@ -652,13 +652,14 @@ namespace rsx
 			m_overlay_manager = g_fxo->init<rsx::overlays::display_manager>(0);
 		}
 
-		state -= cpu_flag::stop + cpu_flag::wait; // TODO: Remove workaround
-
 		if (!_ar)
 		{
+			add_remove_flags({}, cpu_flag::stop); // TODO: Remove workaround
 			return;
 		}
 
+		add_remove_flags(cpu_flag::suspend, cpu_flag::stop);
+
 		serialized = true;
 		save(*_ar);
 
diff --git a/rpcs3/Emu/System.cpp b/rpcs3/Emu/System.cpp
index d3bb9aa9c2..0969cf5a5c 100644
--- a/rpcs3/Emu/System.cpp
+++ b/rpcs3/Emu/System.cpp
@@ -2230,7 +2230,7 @@ game_boot_result Emulator::Load(const std::string& title_id, bool is_disc_patch,
 			}
 		}
 
-		const bool autostart = (std::exchange(m_force_boot, false) || g_cfg.misc.autostart);
+		const bool autostart = m_ar || (std::exchange(m_force_boot, false) || g_cfg.misc.autostart);
 
 		if (IsReady())
 		{
@@ -2333,8 +2333,6 @@ void Emulator::FixGuestTime()
 				}
 			}
 
-			m_ar.reset();
-
 			g_tls_log_prefix = []()
 			{
 				return std::string();
@@ -2349,33 +2347,60 @@ void Emulator::FixGuestTime()
 
 void Emulator::FinalizeRunRequest()
 {
-	auto on_select = [](u32, spu_thread& spu)
+	const bool autostart = !m_ar || !!g_cfg.misc.autostart;
+
+	bs_t<cpu_flag> add_flags = cpu_flag::dbg_global_pause;
+
+	if (autostart)
 	{
+		add_flags -= cpu_flag::dbg_global_pause;
+	}
+
+	auto spu_select = [&](u32, spu_thread& spu)
+	{
+		bs_t<cpu_flag> sub_flags = cpu_flag::stop;
+
 		if (spu.group && spu.index == spu.group->waiter_spu_index)
 		{
-			return;
+			sub_flags -= cpu_flag::stop;
 		}
-
-		if (std::exchange(spu.stop_flag_removal_protection, false))
+		else if (std::exchange(spu.stop_flag_removal_protection, false))
 		{
-			return;
+			sub_flags -= cpu_flag::stop;
 		}
 
-		ensure(spu.state.test_and_reset(cpu_flag::stop));
-		spu.state.notify_one();
+		spu.add_remove_flags(add_flags, sub_flags);
 	};
 
+	auto ppu_select = [&](u32, ppu_thread& ppu)
+	{
+		ppu.state += add_flags;
+	};
+
+	if (auto rsx = g_fxo->try_get<rsx::thread>())
+	{
+		static_cast<cpu_thread*>(rsx)->add_remove_flags(add_flags, cpu_flag::suspend);
+	}
+
 	if (m_savestate_extension_flags1 & SaveStateExtentionFlags1::ShouldCloseMenu)
 	{
 		g_fxo->get<SysutilMenuOpenStatus>().active = true;
 	}
 
-	idm::select<named_thread<spu_thread>>(on_select);
+	idm::select<named_thread<spu_thread>>(spu_select);
+	idm::select<named_thread<ppu_thread>>(ppu_select);
 
 	lv2_obj::make_scheduler_ready();
 
 	m_state.compare_and_swap_test(system_state::starting, system_state::running);
 
+	m_ar.reset();
+
+	if (!autostart)
+	{
+		Pause();
+	}
+
 	if (m_savestate_extension_flags1 & SaveStateExtentionFlags1::ShouldCloseMenu)
 	{
 		std::thread([this, info = GetEmulationIdentifier()]()