diff --git a/src/khoj/database/migrations/0090_alter_khojuser_uuid.py b/src/khoj/database/migrations/0090_alter_khojuser_uuid.py
new file mode 100644
index 00000000..72aeea1b
--- /dev/null
+++ b/src/khoj/database/migrations/0090_alter_khojuser_uuid.py
@@ -0,0 +1,106 @@
+# Generated by Django 5.1.9 on 2025-06-04 01:11
+
+import uuid
+
+from django.db import migrations, models
+
+
+def fix_malformed_uuids(apps, schema_editor):
+    KhojUser = apps.get_model("database", "KhojUser")
+
+    # Track UUID changes for automation cleanup
+    uuid_mappings = {}
+
+    # Handle null or empty user UUIDs
+    for user in KhojUser.objects.filter(uuid__isnull=True):
+        old_uuid = str(user.uuid) if user.uuid else "None"
+        user.uuid = uuid.uuid4()
+        user.save()
+        uuid_mappings[old_uuid] = str(user.uuid)
+
+    # Handle malformed user UUIDs
+    for user in KhojUser.objects.all():
+        current_uuid_val = user.uuid
+        try:
+            if not isinstance(current_uuid_val, uuid.UUID):
+                # Attempt to parse it as UUID. This will catch "None", "null" strings or other malformed hex.
+                uuid.UUID(str(current_uuid_val))
+        except (ValueError, TypeError, AttributeError):
+            old_uuid_str = str(current_uuid_val)
+            new_uuid_obj = uuid.uuid4()
+            user.uuid = new_uuid_obj
+            user.save(
+                update_fields=["uuid"]
+            )  # Important to use update_fields to avoid triggering full save logic if not needed
+            uuid_mappings[old_uuid_str] = str(new_uuid_obj)
+            print(f"Fixed malformed UUID for user (old: '{old_uuid_str}', new: {str(new_uuid_obj)})")
+
+    # Clean up orphaned automations
+    cleanup_orphaned_automations(uuid_mappings)
+
+
+def cleanup_orphaned_automations(uuid_mappings):
+    """Remove automations with malformed UUIDs in job_ids"""
+    from apscheduler.jobstores.base import JobLookupError
+
+    from khoj.utils import state
+
+    if not state.scheduler:
+        return
+
+    all_jobs = state.scheduler.get_jobs()
+    removed_orphaned_count = 0
+    removed_malformed_count = 0
+
+    for job in all_jobs:
+        if job.id.startswith("automation_"):
+            # Extract UUID from job_id: "automation_{uuid}_{query_id}"
+            job_parts = job.id.split("_", 2)
+            if len(job_parts) >= 2:
+                job_uuid = job_parts[1]
+
+                # Check if this UUID was malformed
+                if job_uuid in uuid_mappings:
+                    # Remove orphaned automation
+                    try:
+                        state.scheduler.remove_job(job.id)
+                        removed_orphaned_count += 1
+                        print(f"Removed orphaned automation: {job.id}")
+                    except JobLookupError:
+                        pass  # Job already removed
+
+                # Also remove jobs with clearly malformed UUIDs
+                elif job_uuid in ["None", "null"] or not is_valid_uuid(job_uuid):
+                    try:
+                        state.scheduler.remove_job(job.id)
+                        removed_malformed_count += 1
+                        print(f"Removed automation with malformed UUID: {job.id}")
+                    except JobLookupError:
+                        pass
+
+    if removed_orphaned_count > 0 or removed_malformed_count > 0:
+        print(f"Removed {removed_orphaned_count} orphaned and {removed_malformed_count} malformed automations.")
+
+
+def is_valid_uuid(uuid_string):
+    """Check if string is a valid UUID"""
+    try:
+        uuid.UUID(str(uuid_string))
+        return True
+    except (ValueError, TypeError, AttributeError):
+        return False
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("database", "0089_chatmodel_price_tier_and_more"),
+    ]
+
+    operations = [
+        migrations.RunPython(fix_malformed_uuids, reverse_code=migrations.RunPython.noop),
+        migrations.AlterField(
+            model_name="khojuser",
+            name="uuid",
+            field=models.UUIDField(default=uuid.uuid4, editable=False, unique=True),
+        ),
+    ]
diff --git a/src/khoj/database/models/__init__.py b/src/khoj/database/models/__init__.py
index a854dc91..84948015 100644
--- a/src/khoj/database/models/__init__.py
+++ b/src/khoj/database/models/__init__.py
@@ -137,7 +137,7 @@ class ClientApplication(DbBaseModel):
 
 
 class KhojUser(AbstractUser):
-    uuid = models.UUIDField(models.UUIDField(default=uuid.uuid4, editable=False))
+    uuid = models.UUIDField(default=uuid.uuid4, editable=False, unique=True)
     phone_number = PhoneNumberField(null=True, default=None, blank=True)
     verified_phone_number = models.BooleanField(default=False)
     verified_email = models.BooleanField(default=False)