diff --git a/assay/api-src/org/labkey/api/assay/plate/PlateService.java b/assay/api-src/org/labkey/api/assay/plate/PlateService.java
index 230088b14e7..2633b918c96 100644
--- a/assay/api-src/org/labkey/api/assay/plate/PlateService.java
+++ b/assay/api-src/org/labkey/api/assay/plate/PlateService.java
@@ -30,6 +30,7 @@
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
 import org.labkey.api.services.ServiceRegistry;
+import org.labkey.api.settings.OptionalFeatureService;
 import org.labkey.api.view.ActionURL;
 
 import java.sql.SQLException;
@@ -38,6 +39,7 @@
 public interface PlateService
 {
     long NO_RUNID = -1;
+    String DEPRECATE_PRIMARY_PLATE_SET_FLAG = "primaryPlateSets";
 
     class NameConflictException extends Exception
     {
@@ -272,4 +274,9 @@ interface PlateDetailsResolver
          */
         ActionURL getDetailsURL(Plate plate);
     }
+
+    static boolean isPrimaryPlateSetsEnabled()
+    {
+        return OptionalFeatureService.get().isFeatureEnabled(DEPRECATE_PRIMARY_PLATE_SET_FLAG);
+    }
 }
diff --git a/assay/src/org/labkey/assay/AssayModule.java b/assay/src/org/labkey/assay/AssayModule.java
index 64adeea58f8..062512e22d9 100644
--- a/assay/src/org/labkey/assay/AssayModule.java
+++ b/assay/src/org/labkey/assay/AssayModule.java
@@ -201,6 +201,14 @@ protected void init()
                 false,
                 false,
                 OptionalFeatureService.FeatureType.Deprecated));
+
+        OptionalFeatureService.get().addFeatureFlag(new OptionalFeatureFlag(
+                PlateService.DEPRECATE_PRIMARY_PLATE_SET_FLAG,
+                "Allow for Primary Plate Sets to be created",
+                "Enables the creation of Primary Plate Sets. This option will be removed in a future release of LabKey Server.",
+                false,
+                false,
+                OptionalFeatureService.FeatureType.Deprecated));
     }
 
     @Override
diff --git a/assay/src/org/labkey/assay/data/generator/PlateSetDataGenerator.java b/assay/src/org/labkey/assay/data/generator/PlateSetDataGenerator.java
index 55be38c2279..19a952ad39d 100644
--- a/assay/src/org/labkey/assay/data/generator/PlateSetDataGenerator.java
+++ b/assay/src/org/labkey/assay/data/generator/PlateSetDataGenerator.java
@@ -23,6 +23,7 @@
 import org.labkey.api.assay.plate.AssayPlateMetadataService;
 import org.labkey.api.assay.plate.Plate;
 import org.labkey.api.assay.plate.PlateCustomField;
+import org.labkey.api.assay.plate.PlateService;
 import org.labkey.api.assay.plate.PlateSet;
 import org.labkey.api.assay.plate.PlateSetType;
 import org.labkey.api.assay.plate.PlateType;
@@ -77,6 +78,12 @@ public PlateSetDataGenerator(PipelineJob job, PlateSetDataGenerator.Config confi
 
     public void generatePlateSets()
     {
+        if (!PlateService.isPrimaryPlateSetsEnabled())
+        {
+            _log.error("PlateSetDataGenerator is not able to generate plate sets when primary plate sets are disabled.");
+            return;
+        }
+
         Config config = getConfig();
         if (validateConfiguration(config))
         {
diff --git a/assay/src/org/labkey/assay/plate/PlateManager.java b/assay/src/org/labkey/assay/plate/PlateManager.java
index 5c904cf209a..39c29f1c289 100644
--- a/assay/src/org/labkey/assay/plate/PlateManager.java
+++ b/assay/src/org/labkey/assay/plate/PlateManager.java
@@ -2886,6 +2886,8 @@ public PlateSetImpl createPlateSet(
 
         if (plateSet.getType() == null)
             plateSet.setType(PlateSetType.assay);
+        if (!PlateService.isPrimaryPlateSetsEnabled() && plateSet.getType() == PlateSetType.primary)
+            throw new ValidationException("The primary plate set feature is not enabled.");
 
         try (DbScope.Transaction tx = ensureTransaction())
         {
diff --git a/assay/src/org/labkey/assay/plate/PlateManagerTest.java b/assay/src/org/labkey/assay/plate/PlateManagerTest.java
index 0846613c2c8..dcbb0c1fd73 100644
--- a/assay/src/org/labkey/assay/plate/PlateManagerTest.java
+++ b/assay/src/org/labkey/assay/plate/PlateManagerTest.java
@@ -24,6 +24,7 @@
 import org.labkey.api.assay.plate.Plate;
 import org.labkey.api.assay.plate.PlateCustomField;
 import org.labkey.api.assay.plate.PlateLayoutHandler;
+import org.labkey.api.assay.plate.PlateService;
 import org.labkey.api.assay.plate.PlateSet;
 import org.labkey.api.assay.plate.PlateSetType;
 import org.labkey.api.assay.plate.PlateType;
@@ -55,6 +56,7 @@
 import org.labkey.api.query.QueryUpdateService;
 import org.labkey.api.query.ValidationException;
 import org.labkey.api.security.User;
+import org.labkey.api.settings.OptionalFeatureService;
 import org.labkey.api.util.JunitUtil;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.TestContext;
@@ -99,6 +101,7 @@ public final class PlateManagerTest
     private static Container container;
     private static ExpSampleType sampleType;
     private static User user;
+    private static boolean primaryPlateSetFlag;
 
     private enum PlateMetadataFields
     {
@@ -126,6 +129,10 @@ public static void setupTest() throws Exception
             container.setActiveModules(newActiveModules);
         }
 
+        // Configure optional feature flag
+        primaryPlateSetFlag = OptionalFeatureService.get().isFeatureEnabled(PlateService.DEPRECATE_PRIMARY_PLATE_SET_FLAG);
+        OptionalFeatureService.get().setFeatureEnabled(PlateService.DEPRECATE_PRIMARY_PLATE_SET_FLAG, true, user);
+
         Domain domain = PlateManager.get().getPlateMetadataDomain(container, user);
         if (domain != null)
             domain.delete(user);
@@ -201,11 +208,33 @@ public static void setupTest() throws Exception
     @AfterClass
     public static void cleanup()
     {
+        // Restore optional feature flag
+        OptionalFeatureService.get().setFeatureEnabled(PlateService.DEPRECATE_PRIMARY_PLATE_SET_FLAG, primaryPlateSetFlag, user);
+
         deleteTestContainer();
         container = null;
         user = null;
     }
 
+    @Test
+    public void testDeprecatePrimaryPlateSetFlag()
+    {
+        try
+        {
+            OptionalFeatureService.get().setFeatureEnabled(PlateService.DEPRECATE_PRIMARY_PLATE_SET_FLAG, false, user);
+
+            PlateSetImpl plateSetImpl = new PlateSetImpl();
+            plateSetImpl.setType(PlateSetType.primary);
+            plateSetImpl.setName("testDeprecatePrimaryPlateSetFlag");
+
+            assertCreatePlateSetThrows("The primary plate set feature is not enabled.", plateSetImpl, null, null);
+        }
+        finally
+        {
+            OptionalFeatureService.get().setFeatureEnabled(PlateService.DEPRECATE_PRIMARY_PLATE_SET_FLAG, true, user);
+        }
+    }
+
     @Test
     public void testCreatePlateTemplate() throws Exception
     {