diff --git a/.github/workflows/scripts/linux/appimage-qt.sh b/.github/workflows/scripts/linux/appimage-qt.sh
index 253449b373..f7862358bc 100755
--- a/.github/workflows/scripts/linux/appimage-qt.sh
+++ b/.github/workflows/scripts/linux/appimage-qt.sh
@@ -287,7 +287,7 @@ Plugins = ../lib/plugins
 EOF
 
 echo "Copy desktop/icon..."
-cp "$PCSX2DIR/pcsx2/Resources/AppIcon64.png" "$OUTDIR/PCSX2.png"
+cp "$PCSX2DIR/bin/resources/icons/AppIconLarge.png" "$OUTDIR/PCSX2.png"
 cp "$SCRIPTDIR/pcsx2-qt.desktop" "$OUTDIR/PCSX2.desktop"
 cp "$SCRIPTDIR/AppRun-qt" "$OUTDIR/AppRun"
 
diff --git a/pcsx2-qt/MainWindow.cpp b/pcsx2-qt/MainWindow.cpp
index 9f46afa729..bdc6a1726c 100644
--- a/pcsx2-qt/MainWindow.cpp
+++ b/pcsx2-qt/MainWindow.cpp
@@ -183,7 +183,6 @@ void MainWindow::setupAdditionalUi()
 {
 	const bool show_advanced_settings = QtHost::ShouldShowAdvancedSettings();
 
-	setWindowIcon(QIcon(QStringLiteral("%1/icons/AppIconLarge.png").arg(QtHost::GetResourcesBasePath())));
 	makeIconsMasks(menuBar());
 
 	m_ui.menuDebug->menuAction()->setVisible(show_advanced_settings);
diff --git a/pcsx2-qt/MainWindow.ui b/pcsx2-qt/MainWindow.ui
index df97b7f7db..9373877a40 100644
--- a/pcsx2-qt/MainWindow.ui
+++ b/pcsx2-qt/MainWindow.ui
@@ -16,6 +16,11 @@
   <property name="windowTitle">
    <string>PCSX2</string>
   </property>
+  <property name="windowIcon">
+   <iconset>
+    <normalon>:/icons/AppIcon64.png</normalon>
+   </iconset>
+  </property>
   <widget class="QStackedWidget" name="mainContainer"/>
   <widget class="QMenuBar" name="menuBar">
    <property name="geometry">
@@ -126,10 +131,10 @@
      <property name="title">
       <string>Switch Renderer</string>
      </property>
-    <property name="icon">
-    <iconset theme="brush-line">
-     <normaloff>.</normaloff>.</iconset>
-    </property>
+     <property name="icon">
+      <iconset theme="brush-line">
+       <normaloff>.</normaloff>.</iconset>
+     </property>
     </widget>
     <addaction name="menuDebugSwitchRenderer"/>
     <addaction name="separator"/>
@@ -484,12 +489,12 @@
    </property>
   </action>
   <action name="actionAbout">
-   <property name="text">
-    <string>&amp;About PCSX2...</string>
-   </property>
    <property name="icon">
     <iconset resource="resources/resources.qrc">
-     <normaloff>:/icons/AppIcon.png</normaloff>:/icons/AppIcon.png</iconset>
+     <normaloff>:/icons/AppIcon64.png</normaloff>:/icons/AppIcon64.png</iconset>
+   </property>
+   <property name="text">
+    <string>&amp;About PCSX2...</string>
    </property>
   </action>
   <action name="actionChangeDisc">
diff --git a/pcsx2-qt/SetupWizardDialog.cpp b/pcsx2-qt/SetupWizardDialog.cpp
index 366c45c812..d60586a575 100644
--- a/pcsx2-qt/SetupWizardDialog.cpp
+++ b/pcsx2-qt/SetupWizardDialog.cpp
@@ -169,10 +169,10 @@ void SetupWizardDialog::confirmCancel()
 
 void SetupWizardDialog::setupUi()
 {
-	setWindowIcon(QIcon(QStringLiteral("%1/icons/AppIconLarge.png").arg(QtHost::GetResourcesBasePath())));
-
 	m_ui.setupUi(this);
 
+	m_ui.logo->setPixmap(QPixmap(QStringLiteral("%1/icons/AppIconLarge.png").arg(QtHost::GetResourcesBasePath())));
+
 	m_ui.pages->setCurrentIndex(0);
 
 	m_page_labels[Page_Language] = m_ui.labelLanguage;
diff --git a/pcsx2-qt/SetupWizardDialog.ui b/pcsx2-qt/SetupWizardDialog.ui
index 8ae43f7b2a..773a25f939 100644
--- a/pcsx2-qt/SetupWizardDialog.ui
+++ b/pcsx2-qt/SetupWizardDialog.ui
@@ -13,6 +13,11 @@
   <property name="windowTitle">
    <string>PCSX2 Setup Wizard</string>
   </property>
+  <property name="windowIcon">
+   <iconset>
+    <normalon>:/icons/AppIcon64.png</normalon>
+   </iconset>
+  </property>
   <layout class="QGridLayout" name="gridLayout">
    <property name="horizontalSpacing">
     <number>10</number>
@@ -20,7 +25,7 @@
    <item row="0" column="0">
     <layout class="QVBoxLayout" name="verticalLayout_2">
      <item>
-      <widget class="QLabel" name="label">
+      <widget class="QLabel" name="logo">
        <property name="sizePolicy">
         <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
          <horstretch>0</horstretch>
@@ -33,12 +38,15 @@
          <height>128</height>
         </size>
        </property>
+       <property name="maximumSize">
+        <size>
+         <width>128</width>
+         <height>128</height>
+        </size>
+       </property>
        <property name="text">
         <string/>
        </property>
-       <property name="pixmap">
-        <pixmap resource="resources/resources.qrc">:/icons/AppIcon.png</pixmap>
-       </property>
        <property name="scaledContents">
         <bool>true</bool>
        </property>
diff --git a/pcsx2-qt/resources/icons/AppIcon.png b/pcsx2-qt/resources/icons/AppIcon.png
deleted file mode 100644
index 3d04cd3722..0000000000
Binary files a/pcsx2-qt/resources/icons/AppIcon.png and /dev/null differ
diff --git a/pcsx2/Resources/AppIcon64.png b/pcsx2-qt/resources/icons/AppIcon64.png
similarity index 100%
rename from pcsx2/Resources/AppIcon64.png
rename to pcsx2-qt/resources/icons/AppIcon64.png
diff --git a/pcsx2-qt/resources/resources.qrc b/pcsx2-qt/resources/resources.qrc
index c02307a0dc..eea7134764 100644
--- a/pcsx2-qt/resources/resources.qrc
+++ b/pcsx2-qt/resources/resources.qrc
@@ -1,6 +1,6 @@
 <RCC>
 	<qresource>
-		<file>icons/AppIcon.png</file>
+		<file>icons/AppIcon64.png</file>
 		<file>icons/applications-system-24.png</file>
 		<file>icons/black/index.theme</file>
 		<file>icons/black/svg/arrow-left-right-line.svg</file>
diff --git a/pcsx2/Resources/AppIcon16.png b/pcsx2/Resources/AppIcon16.png
deleted file mode 100644
index 35109d90b0..0000000000
Binary files a/pcsx2/Resources/AppIcon16.png and /dev/null differ
diff --git a/pcsx2/Resources/AppIcon32.png b/pcsx2/Resources/AppIcon32.png
deleted file mode 100644
index 72ab985803..0000000000
Binary files a/pcsx2/Resources/AppIcon32.png and /dev/null differ