diff --git a/.github/workflows/build-windows-executable-app.yaml b/.github/workflows/build-windows-executable-app.yaml
index 3284c10e5..d90c6403a 100644
--- a/.github/workflows/build-windows-executable-app.yaml
+++ b/.github/workflows/build-windows-executable-app.yaml
@@ -359,6 +359,7 @@ jobs:
               </Directory>
               <Directory Id="DesktopFolder" />
             </Directory>
+            <Property Id="WORKSPACES_FOLDER" Value="AppSubFolder" />
         
             <!-- Add components -->
             <Feature Id="MainFeature" Title="Main Application" Level="1">
@@ -391,20 +392,68 @@ jobs:
             <Binary Id="ShowMessageScript" SourceFile="SourceDir/ShowSuccessMessage.vbs" />
             <CustomAction Id="ShowSuccessMessage" BinaryKey="ShowMessageScript" VBScriptCall="" Execute="immediate" Return="check" />
         
+            <!-- Step 1: Pass variables to CustomActionData -->
+            <CustomAction Id="SetWriteWorkspacePathData"
+                          Property="WriteWorkspacePath"
+                          Value="AppSubFolder=[AppSubFolder];WORKSPACES_FOLDER=[WORKSPACES_FOLDER]" />
+
+            <!-- Step 2: Actual PowerShell inline script -->
+            <CustomAction Id="WriteWorkspacePath"
+                Directory="INSTALLFOLDER"
+                Execute="deferred"
+                Impersonate="no"
+                Return="check"
+                ExeCommand="powershell.exe -NoProfile -ExecutionPolicy Bypass -Command &quot;
+                  $props = @{}; ('[CustomActionData]' -split ';') | 
+                  ForEach-Object { $k,$v = $_ -split '=',2; $props[$k]=$v }; 
+                  $settingsPath = Join-Path $props.AppSubFolder 'settings.json'; 
+                  $settings = Get-Content -Raw -Path $settingsPath | ConvertFrom-Json; 
+                  $settings.workspaces_dir = $props.WORKSPACES_FOLDER; 
+                  $settings | ConvertTo-Json -Depth 100 | Set-Content -Path $settingsPath&quot;" />
+
             <!-- Add all Custom Actions -->
             <InstallExecuteSequence>
               <!-- Custom action display success message -->
               <Custom Action="ShowSuccessMessage" After="InstallFinalize">NOT Installed</Custom>
               <!-- Run app directly after installation -->
               <!-- <Custom Action="RunApp" Before="InstallFinalize">NOT REMOVE</Custom> -->
+              <Custom Action="SetWriteWorkspacePathData" Before="WriteWorkspacePath">NOT Installed</Custom>
+              <Custom Action="WriteWorkspacePath" Before="InstallFinalize">NOT Installed</Custom>
             </InstallExecuteSequence>
-        
+
             <!-- Interface options -->
             <UI>
                   <UIRef Id="WixUI_InstallDir" />
                   <UIRef Id="WixUI_ErrorProgressText" />
+
+                  <!-- New Dialog to select workspaces -->
+                  <Dialog Id="ChooseWorkspacesDlg" Width="370" Height="270" Title="!(loc.InstallDirDlg_Title)">
+                    <Control Id="Description" Type="Text" X="25" Y="23" Width="280" Height="15" Transparent="yes" NoPrefix="yes" Text="Click Next to choose default workspaces location or click Change to choose another folder" />
+                    <Control Id="Title" Type="Text" X="15" Y="6" Width="200" Height="15" Transparent="yes" NoPrefix="yes" Text="{\WixUI_Font_Title}Workspaces Folder" />
+                    <Control Id="BannerBitmap" Type="Bitmap" X="0" Y="0" Width="370" Height="44" TabSkip="no" Text="!(loc.InstallDirDlgBannerBitmap)" />
+                    <Control Id="BannerLine" Type="Line" X="0" Y="44" Width="370" Height="0" />
+                    <Control Id="BottomLine" Type="Line" X="0" Y="234" Width="370" Height="0" />
+
+                    <!-- Browse for workspaces folder location -->
+                    <Control Id="WorkspacesFolderLabel" Type="Text" X="20" Y="60" Width="290" Height="30" NoPrefix="yes" Text="Please select a workspace location before continuing installation." />
+                    <Control Id="WorkspacesFolder" Type="PathEdit" X="20" Y="100" Width="320" Height="18" Property="WORKSPACES_FOLDER" Indirect="yes" />
+                    <Control Id="ChangeWorkspacesFolder" Type="PushButton" X="20" Y="120" Width="56" Height="17" Text="Change" />
+
+                    <!-- Navigation Buttons -->
+                    <Control Id="Back" Type="PushButton" X="180" Y="243" Width="56" Height="17" Cancel="yes" Text="!(loc.WixUIBack)" />
+                    <Control Id="Next" Type="PushButton" X="236" Y="243" Width="56" Height="17" Default="yes" Text="!(loc.WixUINext)" />
+                    <Control Id="Cancel" Type="PushButton" X="304" Y="243" Width="56" Height="17" Cancel="yes" Text="!(loc.WixUICancel)">
+                      <Publish Event="SpawnDialog" Value="CancelDlg">1</Publish>
+                    </Control>
+                  </Dialog>
+
+                  <Publish Dialog="LicenseAgreementDlg" Control="Next" Event="NewDialog" Value="ChooseWorkspacesDlg" Order="2">LicenseAccepted = "1"</Publish>
+                  <Publish Dialog="InstallDirDlg" Control="Back" Event="NewDialog" Value="ChooseWorkspacesDlg" Order="2">1</Publish>
+                  <Publish Dialog="ChooseWorkspacesDlg" Control="Next" Event="NewDialog" Value="InstallDirDlg" Order="2">1</Publish>
+                  <Publish Dialog="ChooseWorkspacesDlg" Control="Back" Event="NewDialog" Value="LicenseAgreementDlg" Order="2">1</Publish>
+                  <Publish Dialog="ChooseWorkspacesDlg" Control="ChangeWorkspacesFolder" Property="_BrowseProperty" Value="[WORKSPACES_FOLDER]" Order="2">1</Publish>
+                  <Publish Dialog="ChooseWorkspacesDlg" Control="ChangeWorkspacesFolder" Event="SpawnDialog" Value="BrowseDlg" Order="2">1</Publish>
             </UI> 
-        
             <!-- Provide license; it should exist in the SourceDir folder -->
             <WixVariable Id="WixUILicenseRtf" Value="SourceDir/openms_license.rtf" />
           </Product>