diff --git a/src/EFCore/Metadata/Conventions/ModelCleanupConvention.cs b/src/EFCore/Metadata/Conventions/ModelCleanupConvention.cs
index 33ffd9e2059..20320625645 100644
--- a/src/EFCore/Metadata/Conventions/ModelCleanupConvention.cs
+++ b/src/EFCore/Metadata/Conventions/ModelCleanupConvention.cs
@@ -79,7 +79,8 @@ private void RemoveNavigationlessForeignKeys(IConventionModelBuilder modelBuilde
                 foreach (var foreignKey in entityType.GetDeclaredForeignKeys().ToList())
                 {
                     if (foreignKey.PrincipalToDependent == null
-                        && foreignKey.DependentToPrincipal == null)
+                        && foreignKey.DependentToPrincipal == null
+                        && !foreignKey.GetReferencingSkipNavigations().Any())
                     {
                         entityType.Builder.HasNoRelationship(foreignKey, fromDataAnnotation: true);
                     }
diff --git a/test/EFCore.Tests/ModelBuilding/ManyToManyTestBase.cs b/test/EFCore.Tests/ModelBuilding/ManyToManyTestBase.cs
index 6e2645fcf43..edf69db3f69 100644
--- a/test/EFCore.Tests/ModelBuilding/ManyToManyTestBase.cs
+++ b/test/EFCore.Tests/ModelBuilding/ManyToManyTestBase.cs
@@ -26,6 +26,10 @@ public virtual void Discovers_navigations()
                 modelBuilder.Entity<Product>();
                 modelBuilder.Entity<CategoryBase>();
 
+                var sharedTypeName = nameof(Category) + nameof(Product);
+
+                modelBuilder.SharedTypeEntity<Dictionary<string, object>>(sharedTypeName);
+
                 var model = modelBuilder.FinalizeModel();
 
                 var productType = model.FindEntityType(typeof(Product));
@@ -39,7 +43,7 @@ public virtual void Discovers_navigations()
                 var productCategoryType = categoriesFk.DeclaringEntityType;
 
                 Assert.Equal(typeof(Dictionary<string, object>), productCategoryType.ClrType);
-                Assert.Equal(nameof(Category) + nameof(Product), productCategoryType.Name);
+                Assert.Equal(sharedTypeName, productCategoryType.Name);
                 Assert.Same(categoriesFk, productCategoryType.GetForeignKeys().Last());
                 Assert.Same(productsFk, productCategoryType.GetForeignKeys().First());
                 Assert.Equal(2, productCategoryType.GetForeignKeys().Count());