diff --git a/Source/Core/Core/Boot/Boot_BS2Emu.cpp b/Source/Core/Core/Boot/Boot_BS2Emu.cpp
index 891e7fc324..1f331fbe54 100644
--- a/Source/Core/Core/Boot/Boot_BS2Emu.cpp
+++ b/Source/Core/Core/Boot/Boot_BS2Emu.cpp
@@ -163,7 +163,7 @@ bool CBoot::RunApploader(Core::System& system, const Core::CPUThreadGuard& guard
 
   const bool resume_branch_watch = branch_watch.GetRecordingActive();
   if (system.IsBranchWatchIgnoreApploader())
-    branch_watch.Pause();
+    branch_watch.SetRecordingActive(guard, false);
 
   // Call iAppLoaderEntry.
   DEBUG_LOG_FMT(BOOT, "Call iAppLoaderEntry");
@@ -226,7 +226,7 @@ bool CBoot::RunApploader(Core::System& system, const Core::CPUThreadGuard& guard
   // return
   ppc_state.pc = ppc_state.gpr[3];
 
-  branch_watch.SetRecordingActive(resume_branch_watch);
+  branch_watch.SetRecordingActive(guard, resume_branch_watch);
 
   return true;
 }
diff --git a/Source/Core/Core/Debugger/BranchWatch.h b/Source/Core/Core/Debugger/BranchWatch.h
index fd4cd158ea..32dc28853d 100644
--- a/Source/Core/Core/Debugger/BranchWatch.h
+++ b/Source/Core/Core/Debugger/BranchWatch.h
@@ -117,9 +117,7 @@ public:
   using SelectionInspection = BranchWatchSelectionInspection;
 
   bool GetRecordingActive() const { return m_recording_active; }
-  void SetRecordingActive(bool active) { m_recording_active = active; }
-  void Start() { SetRecordingActive(true); }
-  void Pause() { SetRecordingActive(false); }
+  void SetRecordingActive(const CPUThreadGuard& guard, bool active) { m_recording_active = active; }
   void Clear(const CPUThreadGuard& guard);
 
   void Save(const CPUThreadGuard& guard, std::FILE* file) const;
diff --git a/Source/Core/DolphinQt/Debugger/BranchWatchDialog.cpp b/Source/Core/DolphinQt/Debugger/BranchWatchDialog.cpp
index 39e7748df4..aef6f18cc3 100644
--- a/Source/Core/DolphinQt/Debugger/BranchWatchDialog.cpp
+++ b/Source/Core/DolphinQt/Debugger/BranchWatchDialog.cpp
@@ -516,7 +516,6 @@ BranchWatchDialog::~BranchWatchDialog()
 }
 
 static constexpr int BRANCH_WATCH_TOOL_TIMER_DELAY_MS = 100;
-static constexpr int BRANCH_WATCH_TOOL_TIMER_PAUSE_ONESHOT_MS = 200;
 
 static bool TimerCondition(const Core::BranchWatch& branch_watch, Core::State state)
 {
@@ -537,23 +536,18 @@ void BranchWatchDialog::showEvent(QShowEvent* event)
 
 void BranchWatchDialog::OnStartPause(bool checked) const
 {
+  m_branch_watch.SetRecordingActive(Core::CPUThreadGuard{m_system}, checked);
   if (checked)
   {
-    m_branch_watch.Start();
     m_btn_start_pause->setText(tr("Pause Branch Watch"));
-    // Restart the timer if the situation calls for it, but always turn off single-shot.
-    m_timer->setSingleShot(false);
     if (Core::GetState(m_system) > Core::State::Paused)
       m_timer->start(BRANCH_WATCH_TOOL_TIMER_DELAY_MS);
   }
   else
   {
-    m_branch_watch.Pause();
     m_btn_start_pause->setText(tr("Start Branch Watch"));
-    // Schedule one last update in the future in case Branch Watch is in the middle of a hit.
-    if (Core::GetState(m_system) > Core::State::Paused)
-      m_timer->setInterval(BRANCH_WATCH_TOOL_TIMER_PAUSE_ONESHOT_MS);
-    m_timer->setSingleShot(true);
+    if (m_timer->isActive())
+      m_timer->stop();
   }
   Update();
 }