diff --git a/pwiz_tools/Skyline/Controls/WizardPages.cs b/pwiz_tools/Skyline/Controls/WizardPages.cs
index 07fe21faf6..29b1069a5e 100644
--- a/pwiz_tools/Skyline/Controls/WizardPages.cs
+++ b/pwiz_tools/Skyline/Controls/WizardPages.cs
@@ -50,6 +50,17 @@ protected override bool ProcessCmdKey(ref Message msg, Keys keyData)
             return base.ProcessCmdKey(ref msg, keyData);
         }
     }
+
+    public class WizardPageControl : UserControl
+    {
+        /// <summary>
+        /// Allow controls in a wizard to preempt close requests by the wizard's form. Returns true iff the close request should continue, false if it should be canceled.
+        /// </summary>
+        public virtual bool CanWizardClose()
+        {
+            return true;
+        }
+    }
 }
 
 
diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs
index 346dc039fe..7590dd02de 100644
--- a/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs
+++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/ImportPeptideSearchDlg.cs
@@ -226,6 +226,12 @@ private static void AddPageControl<TControl>(TControl pageControl, TabPage tabPa
             tabPage.Controls.Add(pageControl);
         }
 
+        private UserControl GetPageControl(TabPage tabPage)
+        {
+            // Assume each tabPage only has a single UserControl; if that changes this function will need to be updated
+            return tabPage.Controls.OfType<UserControl>().SingleOrDefault();
+        }
+
         public SrmDocument Document
         {
             get
@@ -998,7 +1004,6 @@ private void InitiateSearch()
             btnNext.Enabled = false;
             btnCancel.Enabled = false;
             btnBack.Enabled = false;
-            ControlBox = false;
 
             AbstractDdaConverter.MsdataFileFormat requiredFormat =
                 IsFeatureDetectionWorkflow
@@ -1085,7 +1090,6 @@ private void SearchControlSearchFinished(bool success)
         {
             btnCancel.Enabled = true;
             btnBack.Enabled = true;
-            ControlBox = true;
             btnNext.Enabled = success;
         }
 
@@ -1484,8 +1488,21 @@ public void CloseWizard(DialogResult result)
             DialogResult = result;
         }
 
+        private bool CanWizardClose()
+        {
+            var wizardPageControl = GetPageControl(wizardPagesImportPeptideSearch.SelectedTab) as WizardPageControl;
+            return wizardPageControl == null || wizardPageControl.CanWizardClose();
+        }
+
         protected override void OnFormClosing(FormClosingEventArgs e)
         {
+            // Ask current WizardPageControl if wizard is in a good state to close
+            if (!CanWizardClose())
+            {
+                e.Cancel = true;
+                return;
+            }
+
             // Close file handles to the peptide search library
             ImportPeptideSearch.ClosePeptideSearchLibraryStreams(Document);
 
diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/PeptideSearchResources.designer.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/PeptideSearchResources.designer.cs
index 5ef37e3264..7faf49c743 100644
--- a/pwiz_tools/Skyline/FileUI/PeptideSearch/PeptideSearchResources.designer.cs
+++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/PeptideSearchResources.designer.cs
@@ -775,6 +775,15 @@ public static string MessageBoxHelper_ValidateAdductListTextBox__0__must_contain
             }
         }
         
+        /// <summary>
+        ///   Looks up a localized string similar to Cannot close wizard while the search is running. Do you want to cancel the search?.
+        /// </summary>
+        public static string SearchControl_CanWizardClose_Cannot_close_wizard_while_the_search_is_running_ {
+            get {
+                return ResourceManager.GetString("SearchControl_CanWizardClose_Cannot_close_wizard_while_the_search_is_running_", resourceCulture);
+            }
+        }
+        
         /// <summary>
         ///   Looks up a localized string similar to Additional Settings.
         /// </summary>
diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/PeptideSearchResources.resx b/pwiz_tools/Skyline/FileUI/PeptideSearch/PeptideSearchResources.resx
index a46314ad4a..d221116c91 100644
--- a/pwiz_tools/Skyline/FileUI/PeptideSearch/PeptideSearchResources.resx
+++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/PeptideSearchResources.resx
@@ -362,4 +362,7 @@ Click 'Retry' to try building again after placing the original spectrum files in
   <data name="ImportPeptideSearchDlg_NextPage_Adding_detected_features_to_document" xml:space="preserve">
     <value>Adding detected features to document</value>
   </data>
+  <data name="SearchControl_CanWizardClose_Cannot_close_wizard_while_the_search_is_running_" xml:space="preserve">
+      <value>Cannot close wizard while the search is running. Do you want to cancel the search?</value>
+  </data>
 </root>
\ No newline at end of file
diff --git a/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchControl.cs b/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchControl.cs
index 04e78d3845..30874b083c 100644
--- a/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchControl.cs
+++ b/pwiz_tools/Skyline/FileUI/PeptideSearch/SearchControl.cs
@@ -27,12 +27,13 @@
 using pwiz.Common.Controls;
 using pwiz.Common.SystemUtil;
 using pwiz.Skyline.Alerts;
+using pwiz.Skyline.Controls;
 using pwiz.Skyline.Util;
 using pwiz.Skyline.Util.Extensions;
 
 namespace pwiz.Skyline.FileUI.PeptideSearch
 {
-    public abstract partial class SearchControl : UserControl, IProgressMonitor
+    public abstract partial class SearchControl : WizardPageControl, IProgressMonitor
     {
         public Action<IProgressStatus> UpdateUI;
 
@@ -266,6 +267,22 @@ public void Cancel()
             btnCancel.Enabled = false;
         }
 
+        public override bool CanWizardClose()
+        {
+            if (btnCancel.Enabled)
+            {
+                if (DialogResult.Yes == MessageDlg.Show(Parent,
+                        PeptideSearchResources.SearchControl_CanWizardClose_Cannot_close_wizard_while_the_search_is_running_, false,
+                        MessageBoxButtons.YesNo))
+                {
+                    Cancel();
+                    SearchFinished += _ => ParentForm?.Close();
+                }
+                return false;
+            }
+            return base.CanWizardClose();
+        }
+
         private void btnCancel_Click(object sender, EventArgs e)
         {
             Cancel();
diff --git a/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs b/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs
index 9d2e835e51..e58486c703 100644
--- a/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs
+++ b/pwiz_tools/Skyline/TestFunctional/DdaSearchTest.cs
@@ -407,13 +407,20 @@ private void TestSearch()
             {
                 importPeptideSearchDlg.SearchControl.SearchFinished += (success) => searchSucceeded = success;
                 importPeptideSearchDlg.BuildPepSearchLibControl.IncludeAmbiguousMatches = true;
-
-                // Cancel search
-                if (!errorExpected)
-                    importPeptideSearchDlg.SearchControl.Cancel();
             });
 
-            if (errorExpected)
+            if (!errorExpected)
+            {
+                SkylineWindow.BeginInvoke(new Action(importPeptideSearchDlg.Close)); // try to close (don't wait for return)
+                var cannotCloseDuringSearchDlg = WaitForOpenForm<MessageDlg>();
+                Assert.AreEqual(PeptideSearchResources.SearchControl_CanWizardClose_Cannot_close_wizard_while_the_search_is_running_,
+                    cannotCloseDuringSearchDlg.Message);
+                OkDialog(cannotCloseDuringSearchDlg, cannotCloseDuringSearchDlg.ClickNo);
+
+                // Cancel search (but don't close wizard)
+                RunUI(importPeptideSearchDlg.SearchControl.Cancel);
+            }
+            else // errorExpected
             {
                 var fastaFileNotFoundDlg = WaitForOpenForm<MessageDlg>();
                 var expectedMsg = new FileNotFoundException(GetSystemResourceString("IO.FileNotFound_FileName", GetTestPath(TestSettings.FastaFilename))).Message;