diff --git a/Source/Core/DolphinQt/Config/Mapping/MappingButton.cpp b/Source/Core/DolphinQt/Config/Mapping/MappingButton.cpp
index d0e1ce4bbe..24e7be9bf8 100644
--- a/Source/Core/DolphinQt/Config/Mapping/MappingButton.cpp
+++ b/Source/Core/DolphinQt/Config/Mapping/MappingButton.cpp
@@ -65,8 +65,9 @@ static QString RefToDisplayString(ControlReference* ref)
   return expression;
 }
 
-MappingButton::MappingButton(MappingWidget* parent, ControlReference* ref)
-    : ElidedButton(RefToDisplayString(ref)), m_mapping_window(parent->GetParent()), m_reference(ref)
+MappingButton::MappingButton(MappingWidget* parent, ControlReference* ref, ControlType control_type)
+    : ElidedButton{RefToDisplayString(ref)}, m_mapping_window{parent->GetParent()},
+      m_reference{ref}, m_control_type{control_type}
 {
   if (m_reference->IsInput())
   {
@@ -141,3 +142,8 @@ ControlReference* MappingButton::GetControlReference()
 {
   return m_reference;
 }
+
+auto MappingButton::GetControlType() const -> ControlType
+{
+  return m_control_type;
+}
diff --git a/Source/Core/DolphinQt/Config/Mapping/MappingButton.h b/Source/Core/DolphinQt/Config/Mapping/MappingButton.h
index 733bdf3e9e..7cac489ad0 100644
--- a/Source/Core/DolphinQt/Config/Mapping/MappingButton.h
+++ b/Source/Core/DolphinQt/Config/Mapping/MappingButton.h
@@ -15,9 +15,17 @@ class MappingButton : public ElidedButton
 {
   Q_OBJECT
 public:
-  MappingButton(MappingWidget* widget, ControlReference* ref);
+  enum class ControlType
+  {
+    NormalInput,
+    ModifierInput,
+    Output,
+  };
+
+  MappingButton(MappingWidget* widget, ControlReference* ref, ControlType type);
 
   ControlReference* GetControlReference();
+  ControlType GetControlType() const;
 
 signals:
   void ConfigChanged();
@@ -32,4 +40,5 @@ private:
 
   MappingWindow* const m_mapping_window;
   ControlReference* const m_reference;
+  const ControlType m_control_type;
 };
diff --git a/Source/Core/DolphinQt/Config/Mapping/MappingCommon.cpp b/Source/Core/DolphinQt/Config/Mapping/MappingCommon.cpp
index 54a0db59ef..d94502b104 100644
--- a/Source/Core/DolphinQt/Config/Mapping/MappingCommon.cpp
+++ b/Source/Core/DolphinQt/Config/Mapping/MappingCommon.cpp
@@ -25,6 +25,11 @@ constexpr auto INPUT_DETECT_MAXIMUM_TIME = std::chrono::seconds(5);
 // Ignore the mouse-click when queuing more buttons with "alternate mappings" enabled.
 constexpr auto INPUT_DETECT_ENDING_IGNORE_TIME = std::chrono::milliseconds(50);
 
+bool ContainsAnalogInput(const ciface::Core::InputDetector::Results& results)
+{
+  return std::ranges::any_of(results, [](auto& detection) { return detection.smoothness > 1; });
+}
+
 class MappingProcessor : public QWidget
 {
 public:
@@ -75,24 +80,40 @@ public:
     m_input_detector->Update(INPUT_DETECT_INITIAL_TIME, confirmation_time,
                              INPUT_DETECT_MAXIMUM_TIME);
 
-    if (m_input_detector->IsComplete())
-    {
-      auto* const button = m_clicked_mapping_buttons.back();
+    if (!m_input_detector->IsComplete())
+      return;
 
-      if (!FinalizeMapping(m_input_detector->TakeResults()))
+    auto* const button = m_clicked_mapping_buttons.front();
+
+    auto results = m_input_detector->TakeResults();
+    if (!FinalizeMapping(&results))
+    {
+      // No inputs detected. Cancel this and any other queued mappings.
+      CancelMapping();
+    }
+    else if (m_parent->IsIterativeMappingEnabled() && m_clicked_mapping_buttons.empty())
+    {
+      button->QueueNextButtonMapping();
+
+      if (m_clicked_mapping_buttons.empty())
+        return;
+
+      // Skip "Modifier" mappings when using analog inputs.
+      auto* next_button = m_clicked_mapping_buttons.front();
+      if (next_button->GetControlType() == MappingButton::ControlType::ModifierInput &&
+          ContainsAnalogInput(results))
       {
-        // No inputs detected. Cancel this and any other queued mappings.
-        CancelMapping();
-      }
-      else if (m_parent->IsIterativeMappingEnabled() && m_clicked_mapping_buttons.empty())
-      {
-        button->QueueNextButtonMapping();
+        // Clear "Modifier" mapping and queue the next button.
+        SetButtonExpression(next_button, "");
+        UnQueueInputDetection(next_button);
+        next_button->QueueNextButtonMapping();
       }
     }
   }
 
-  bool FinalizeMapping(ciface::Core::InputDetector::Results detections)
+  bool FinalizeMapping(ciface::Core::InputDetector::Results* detections_ptr)
   {
+    auto& detections = *detections_ptr;
     if (!ciface::MappingCommon::ContainsCompleteDetection(detections))
       return false;
 
@@ -100,18 +121,22 @@ public:
 
     const auto& default_device = m_parent->GetController()->GetDefaultDevice();
     auto& button = m_clicked_mapping_buttons.front();
-    auto* const control_reference = button->GetControlReference();
+    SetButtonExpression(
+        button, BuildExpression(detections, default_device, ciface::MappingCommon::Quote::On));
 
-    control_reference->SetExpression(
-        BuildExpression(detections, default_device, ciface::MappingCommon::Quote::On));
-    m_parent->Save();
-
-    m_parent->GetController()->UpdateSingleControlReference(g_controller_interface,
-                                                            control_reference);
     UnQueueInputDetection(button);
     return true;
   }
 
+  void SetButtonExpression(MappingButton* button, const std::string& expression)
+  {
+    auto* const control_reference = button->GetControlReference();
+    control_reference->SetExpression(expression);
+    m_parent->Save();
+    m_parent->GetController()->UpdateSingleControlReference(g_controller_interface,
+                                                            control_reference);
+  }
+
   void UpdateInputDetectionStartTimer()
   {
     m_input_detector.reset();
@@ -146,7 +171,7 @@ public:
       auto results = m_input_detector->TakeResults();
       ciface::MappingCommon::RemoveDetectionsAfterTimePoint(
           &results, ciface::Core::DeviceContainer::Clock::now() - INPUT_DETECT_ENDING_IGNORE_TIME);
-      FinalizeMapping(std::move(results));
+      FinalizeMapping(&results);
     }
     UpdateInputDetectionStartTimer();
   }
diff --git a/Source/Core/DolphinQt/Config/Mapping/MappingWidget.cpp b/Source/Core/DolphinQt/Config/Mapping/MappingWidget.cpp
index 442fff464f..036e9c512e 100644
--- a/Source/Core/DolphinQt/Config/Mapping/MappingWidget.cpp
+++ b/Source/Core/DolphinQt/Config/Mapping/MappingWidget.cpp
@@ -313,7 +313,16 @@ QGroupBox* MappingWidget::CreateControlsBox(const QString& name, ControllerEmu::
 void MappingWidget::CreateControl(const ControllerEmu::Control* control, QFormLayout* layout,
                                   bool indicator)
 {
-  auto* const button = new MappingButton(this, control->control_ref.get());
+  // I know this check is terrible, but it's just UI code.
+  const bool is_modifier = control->name == "Modifier";
+
+  using ControlType = MappingButton::ControlType;
+  const auto control_type =
+      control->control_ref->IsInput() ?
+          (is_modifier ? ControlType::ModifierInput : ControlType::NormalInput) :
+          ControlType::Output;
+
+  auto* const button = new MappingButton(this, control->control_ref.get(), control_type);
 
   if (control->control_ref->IsInput())
   {