diff --git a/posthog/hogql/database/test/test_database.py b/posthog/hogql/database/test/test_database.py
index 616d1b1d8e57f..ddc5901a637d8 100644
--- a/posthog/hogql/database/test/test_database.py
+++ b/posthog/hogql/database/test/test_database.py
@@ -111,6 +111,27 @@ def test_serialize_database_warehouse_table_s3(self):
         assert field.type == "string"
         assert field.schema_valid is True
 
+    def test_serialize_database_warehouse_with_deleted_joins(self):
+        DataWarehouseJoin.objects.create(
+            team=self.team,
+            source_table_name="events",
+            source_table_key="event",
+            joining_table_name="groups",
+            joining_table_key="key",
+            field_name="some_field",
+            deleted=True,
+        )
+
+        db = create_hogql_database(team_id=self.team.pk)
+
+        serialized_database = serialize_database(HogQLContext(team_id=self.team.pk, database=db))
+
+        events_table = serialized_database.get("events")
+        assert events_table is not None
+
+        joined_field = events_table.fields.get("some_field")
+        assert joined_field is None
+
     def test_serialize_database_warehouse_table_s3_with_hyphens(self):
         credentials = DataWarehouseCredential.objects.create(access_key="blah", access_secret="blah", team=self.team)
         DataWarehouseTable.objects.create(
diff --git a/posthog/warehouse/api/saved_query.py b/posthog/warehouse/api/saved_query.py
index ac8c8e53022dd..2d8ef156aa6b0 100644
--- a/posthog/warehouse/api/saved_query.py
+++ b/posthog/warehouse/api/saved_query.py
@@ -4,6 +4,7 @@
 import structlog
 from asgiref.sync import async_to_sync
 from django.db import transaction
+from django.db.models import Q
 from rest_framework import exceptions, filters, request, response, serializers, status, viewsets
 from rest_framework.decorators import action
 
@@ -155,8 +156,11 @@ def safely_get_queryset(self, queryset):
 
     def destroy(self, request: request.Request, *args: Any, **kwargs: Any) -> response.Response:
         instance: DataWarehouseSavedQuery = self.get_object()
-        DataWarehouseJoin.objects.filter(source_table_name=instance.name).delete()
-        DataWarehouseJoin.objects.filter(joining_table_name=instance.name).delete()
+
+        for join in DataWarehouseJoin.objects.filter(
+            Q(team_id=instance.team_id) & (Q(source_table_name=instance.name) | Q(joining_table_name=instance.name))
+        ).exclude(deleted=True):
+            join.soft_delete()
 
         if instance.table is not None:
             instance.table.soft_delete()
diff --git a/posthog/warehouse/data_load/source_templates.py b/posthog/warehouse/data_load/source_templates.py
index 17dd1b7b9fecd..5a7d515bc8536 100644
--- a/posthog/warehouse/data_load/source_templates.py
+++ b/posthog/warehouse/data_load/source_templates.py
@@ -7,23 +7,31 @@
 
 @database_sync_to_async
 def database_operations(team_id: int, table_prefix: str) -> None:
-    customer_join_exists = DataWarehouseJoin.objects.filter(
-        team_id=team_id,
-        source_table_name="persons",
-        source_table_key="properties.email",
-        joining_table_name=f"{table_prefix}stripe_customer",
-        joining_table_key="email",
-        field_name=f"{table_prefix}stripe_customer",
-    ).exists()
+    customer_join_exists = (
+        DataWarehouseJoin.objects.filter(
+            team_id=team_id,
+            source_table_name="persons",
+            source_table_key="properties.email",
+            joining_table_name=f"{table_prefix}stripe_customer",
+            joining_table_key="email",
+            field_name=f"{table_prefix}stripe_customer",
+        )
+        .exclude(deleted=True)
+        .exists()
+    )
 
-    invoice_join_exists = DataWarehouseJoin.objects.filter(
-        team_id=team_id,
-        source_table_name="persons",
-        source_table_key="properties.email",
-        joining_table_name=f"{table_prefix}stripe_invoice",
-        joining_table_key="customer_email",
-        field_name=f"{table_prefix}stripe_invoice",
-    ).exists()
+    invoice_join_exists = (
+        DataWarehouseJoin.objects.filter(
+            team_id=team_id,
+            source_table_name="persons",
+            source_table_key="properties.email",
+            joining_table_name=f"{table_prefix}stripe_invoice",
+            joining_table_key="customer_email",
+            field_name=f"{table_prefix}stripe_invoice",
+        )
+        .exclude(deleted=True)
+        .exists()
+    )
 
     if not customer_join_exists:
         DataWarehouseJoin.objects.create(
diff --git a/posthog/warehouse/models/join.py b/posthog/warehouse/models/join.py
index 000b1ba34f9b2..febbf0182f1ca 100644
--- a/posthog/warehouse/models/join.py
+++ b/posthog/warehouse/models/join.py
@@ -1,6 +1,6 @@
 from typing import Optional
 from warnings import warn
-
+from datetime import datetime
 from django.db import models
 
 from posthog.hogql.ast import SelectQuery
@@ -41,6 +41,11 @@ class DataWarehouseJoin(CreatedMetaFields, UUIDModel, DeletedMetaFields):
     joining_table_key = models.CharField(max_length=400)
     field_name = models.CharField(max_length=400)
 
+    def soft_delete(self):
+        self.deleted = True
+        self.deleted_at = datetime.now()
+        self.save()
+
     def join_function(
         self, override_source_table_key: Optional[str] = None, override_joining_table_key: Optional[str] = None
     ):
diff --git a/posthog/warehouse/models/table.py b/posthog/warehouse/models/table.py
index 928ca1596456c..a83cf2735f56e 100644
--- a/posthog/warehouse/models/table.py
+++ b/posthog/warehouse/models/table.py
@@ -104,8 +104,10 @@ class TableFormat(models.TextChoices):
     def soft_delete(self):
         from posthog.warehouse.models.join import DataWarehouseJoin
 
-        DataWarehouseJoin.objects.filter(source_table_name=self.name).delete()
-        DataWarehouseJoin.objects.filter(joining_table_name=self.name).delete()
+        for join in DataWarehouseJoin.objects.filter(
+            Q(team_id=self.team.pk) & (Q(source_table_name=self.name) | Q(joining_table_name=self.name))
+        ).exclude(deleted=True):
+            join.soft_delete()
 
         self.deleted = True
         self.deleted_at = datetime.now()