diff --git a/Source/Core/DolphinQt/CMakeLists.txt b/Source/Core/DolphinQt/CMakeLists.txt
index 930e95820b..78a842f2bc 100644
--- a/Source/Core/DolphinQt/CMakeLists.txt
+++ b/Source/Core/DolphinQt/CMakeLists.txt
@@ -337,6 +337,8 @@ add_executable(dolphin-emu
   TAS/StickWidget.h
   TAS/TASCheckBox.cpp
   TAS/TASCheckBox.h
+  TAS/TASControlState.cpp
+  TAS/TASControlState.h
   TAS/TASInputWindow.cpp
   TAS/TASInputWindow.h
   TAS/TASSlider.cpp
diff --git a/Source/Core/DolphinQt/DolphinQt.vcxproj b/Source/Core/DolphinQt/DolphinQt.vcxproj
index f776feceed..76b01c95d7 100644
--- a/Source/Core/DolphinQt/DolphinQt.vcxproj
+++ b/Source/Core/DolphinQt/DolphinQt.vcxproj
@@ -207,6 +207,7 @@
     <ClCompile Include="TAS\StickWidget.cpp" />
     <ClCompile Include="TAS\TASCheckBox.cpp" />
     <ClCompile Include="TAS\TASInputWindow.cpp" />
+    <ClCompile Include="TAS\TASControlState.cpp" />
     <ClCompile Include="TAS\TASSlider.cpp" />
     <ClCompile Include="TAS\WiiTASInputWindow.cpp" />
     <ClCompile Include="ToolBar.cpp" />
@@ -242,6 +243,7 @@
     <ClInclude Include="QtUtils\WrapInScrollArea.h" />
     <ClInclude Include="ResourcePackManager.h" />
     <ClInclude Include="Resources.h" />
+    <ClInclude Include="TAS\TASControlState.h" />
     <ClInclude Include="TAS\TASSlider.h" />
     <ClInclude Include="Translation.h" />
     <ClInclude Include="WiiUpdate.h" />
diff --git a/Source/Core/DolphinQt/TAS/TASCheckBox.cpp b/Source/Core/DolphinQt/TAS/TASCheckBox.cpp
index 29a7171f47..32d1b3b0b0 100644
--- a/Source/Core/DolphinQt/TAS/TASCheckBox.cpp
+++ b/Source/Core/DolphinQt/TAS/TASCheckBox.cpp
@@ -6,23 +6,34 @@
 #include <QMouseEvent>
 
 #include "Core/Movie.h"
+#include "DolphinQt/QtUtils/QueueOnObject.h"
 #include "DolphinQt/TAS/TASInputWindow.h"
 
 TASCheckBox::TASCheckBox(const QString& text, TASInputWindow* parent)
     : QCheckBox(text, parent), m_parent(parent)
 {
   setTristate(true);
+
+  connect(this, &TASCheckBox::stateChanged, this, &TASCheckBox::OnUIValueChanged);
 }
 
 bool TASCheckBox::GetValue() const
 {
-  if (checkState() == Qt::PartiallyChecked)
+  Qt::CheckState check_state = static_cast<Qt::CheckState>(m_state.GetValue());
+
+  if (check_state == Qt::PartiallyChecked)
   {
     const u64 frames_elapsed = Movie::GetCurrentFrame() - m_frame_turbo_started;
     return static_cast<int>(frames_elapsed % m_turbo_total_frames) < m_turbo_press_frames;
   }
 
-  return isChecked();
+  return check_state != Qt::Unchecked;
+}
+
+void TASCheckBox::OnControllerValueChanged(bool new_value)
+{
+  if (m_state.OnControllerValueChanged(new_value ? Qt::Checked : Qt::Unchecked))
+    QueueOnObject(this, &TASCheckBox::ApplyControllerValueChange);
 }
 
 void TASCheckBox::mousePressEvent(QMouseEvent* event)
@@ -44,3 +55,14 @@ void TASCheckBox::mousePressEvent(QMouseEvent* event)
   m_turbo_total_frames = m_turbo_press_frames + m_parent->GetTurboReleaseFrames();
   setCheckState(Qt::PartiallyChecked);
 }
+
+void TASCheckBox::OnUIValueChanged(int new_value)
+{
+  m_state.OnUIValueChanged(static_cast<u16>(new_value));
+}
+
+void TASCheckBox::ApplyControllerValueChange()
+{
+  const QSignalBlocker blocker(this);
+  setCheckState(static_cast<Qt::CheckState>(m_state.ApplyControllerValueChange()));
+}
diff --git a/Source/Core/DolphinQt/TAS/TASCheckBox.h b/Source/Core/DolphinQt/TAS/TASCheckBox.h
index afec671194..3af68d43b2 100644
--- a/Source/Core/DolphinQt/TAS/TASCheckBox.h
+++ b/Source/Core/DolphinQt/TAS/TASCheckBox.h
@@ -5,6 +5,8 @@
 
 #include <QCheckBox>
 
+#include "DolphinQt/TAS/TASControlState.h"
+
 class QMouseEvent;
 class TASInputWindow;
 
@@ -14,13 +16,21 @@ class TASCheckBox : public QCheckBox
 public:
   explicit TASCheckBox(const QString& text, TASInputWindow* parent);
 
+  // Can be called from the CPU thread
   bool GetValue() const;
+  // Must be called from the CPU thread
+  void OnControllerValueChanged(bool new_value);
 
 protected:
   void mousePressEvent(QMouseEvent* event) override;
 
+private slots:
+  void OnUIValueChanged(int new_value);
+  void ApplyControllerValueChange();
+
 private:
   const TASInputWindow* m_parent;
+  TASControlState m_state;
   int m_frame_turbo_started = 0;
   int m_turbo_press_frames = 0;
   int m_turbo_total_frames = 0;
diff --git a/Source/Core/DolphinQt/TAS/TASControlState.cpp b/Source/Core/DolphinQt/TAS/TASControlState.cpp
new file mode 100644
index 0000000000..fd0c209aa6
--- /dev/null
+++ b/Source/Core/DolphinQt/TAS/TASControlState.cpp
@@ -0,0 +1,58 @@
+// Copyright 2023 Dolphin Emulator Project
+// SPDX-License-Identifier: GPL-2.0-or-later
+
+#include "DolphinQt/TAS/TASControlState.h"
+
+#include <atomic>
+
+#include "Common/CommonTypes.h"
+
+u16 TASControlState::GetValue() const
+{
+  const State ui_thread_state = m_ui_thread_state.load(std::memory_order_relaxed);
+  const State cpu_thread_state = m_cpu_thread_state.load(std::memory_order_relaxed);
+
+  return (ui_thread_state.version != cpu_thread_state.version ? cpu_thread_state : ui_thread_state)
+      .value;
+}
+
+bool TASControlState::OnControllerValueChanged(u16 new_value)
+{
+  const State cpu_thread_state = m_cpu_thread_state.load(std::memory_order_relaxed);
+
+  if (cpu_thread_state.value == new_value)
+  {
+    // The CPU thread state is already up to date with the controller. No need to do anything
+    return false;
+  }
+
+  const State new_state{static_cast<u16>(cpu_thread_state.version + 1), new_value};
+  m_cpu_thread_state.store(new_state, std::memory_order_relaxed);
+
+  return true;
+}
+
+void TASControlState::OnUIValueChanged(u16 new_value)
+{
+  const State ui_thread_state = m_ui_thread_state.load(std::memory_order_relaxed);
+
+  const State new_state{ui_thread_state.version, new_value};
+  m_ui_thread_state.store(new_state, std::memory_order_relaxed);
+}
+
+u16 TASControlState::ApplyControllerValueChange()
+{
+  const State ui_thread_state = m_ui_thread_state.load(std::memory_order_relaxed);
+  const State cpu_thread_state = m_cpu_thread_state.load(std::memory_order_relaxed);
+
+  if (ui_thread_state.version == cpu_thread_state.version)
+  {
+    // The UI thread state is already up to date with the CPU thread. No need to do anything
+    return ui_thread_state.value;
+  }
+  else
+  {
+    m_ui_thread_state.store(cpu_thread_state, std::memory_order_relaxed);
+    return cpu_thread_state.value;
+  }
+}
diff --git a/Source/Core/DolphinQt/TAS/TASControlState.h b/Source/Core/DolphinQt/TAS/TASControlState.h
new file mode 100644
index 0000000000..b53c7f95f9
--- /dev/null
+++ b/Source/Core/DolphinQt/TAS/TASControlState.h
@@ -0,0 +1,43 @@
+// Copyright 2023 Dolphin Emulator Project
+// SPDX-License-Identifier: GPL-2.0-or-later
+
+#pragma once
+
+#include <atomic>
+
+#include "Common/CommonTypes.h"
+
+class TASControlState
+{
+public:
+  // Call this from the CPU thread to get the current value. (This function can also safely be
+  // called from the UI thread, but you're effectively just getting the value the UI control has.)
+  u16 GetValue() const;
+  // Call this from the CPU thread when the controller state changes.
+  // If the return value is true, queue up a call to ApplyControllerChangeValue on the UI thread.
+  bool OnControllerValueChanged(u16 new_value);
+  // Call this from the UI thread when the user changes the value using the UI.
+  void OnUIValueChanged(u16 new_value);
+  // Call this from the UI thread after OnControllerValueChanged returns true,
+  // and set the state of the UI control to the return value.
+  u16 ApplyControllerValueChange();
+
+private:
+  // A description of how threading is handled: The UI thread can update its copy of the state
+  // whenever it wants to, and must *not* increment the version when doing so. The CPU thread can
+  // update its copy of the state whenever it wants to, and *must* increment the version when doing
+  // so. When the CPU thread updates its copy of the state, the UI thread should then (possibly
+  // after a delay) mirror the change by copying the CPU thread's state to the UI thread's state.
+  // This mirroring is the only way for the version number stored in the UI thread's state to
+  // change. The version numbers of the two copies can be compared to check if the UI thread's view
+  // of what has happened on the CPU thread is up to date.
+
+  struct State
+  {
+    u16 version = 0;
+    u16 value = 0;
+  };
+
+  std::atomic<State> m_ui_thread_state;
+  std::atomic<State> m_cpu_thread_state;
+};
diff --git a/Source/Core/DolphinQt/TAS/TASInputWindow.cpp b/Source/Core/DolphinQt/TAS/TASInputWindow.cpp
index 0054043a8e..61e37e5238 100644
--- a/Source/Core/DolphinQt/TAS/TASInputWindow.cpp
+++ b/Source/Core/DolphinQt/TAS/TASInputWindow.cpp
@@ -239,18 +239,7 @@ std::optional<ControlState> TASInputWindow::GetButton(TASCheckBox* checkbox,
 {
   const bool pressed = std::llround(controller_state) > 0;
   if (m_use_controller->isChecked())
-  {
-    if (pressed)
-    {
-      m_checkbox_set_by_controller[checkbox] = true;
-      QueueOnObjectBlocking(checkbox, [checkbox] { checkbox->setChecked(true); });
-    }
-    else if (m_checkbox_set_by_controller.count(checkbox) && m_checkbox_set_by_controller[checkbox])
-    {
-      m_checkbox_set_by_controller[checkbox] = false;
-      QueueOnObjectBlocking(checkbox, [checkbox] { checkbox->setChecked(false); });
-    }
-  }
+    checkbox->OnControllerValueChanged(pressed);
 
   return checkbox->GetValue() ? 1.0 : 0.0;
 }
diff --git a/Source/Core/DolphinQt/TAS/TASInputWindow.h b/Source/Core/DolphinQt/TAS/TASInputWindow.h
index e1f56e0235..104cb28fe9 100644
--- a/Source/Core/DolphinQt/TAS/TASInputWindow.h
+++ b/Source/Core/DolphinQt/TAS/TASInputWindow.h
@@ -79,6 +79,5 @@ private:
   std::optional<ControlState> GetSpinBox(QSpinBox* spin, u16 zero, ControlState controller_state,
                                          ControlState scale);
 
-  std::map<TASCheckBox*, bool> m_checkbox_set_by_controller;
   std::map<QSpinBox*, u16> m_spinbox_most_recent_values;
 };