diff --git a/src/EFCore.PG/Migrations/Internal/NpgsqlHistoryRepository.cs b/src/EFCore.PG/Migrations/Internal/NpgsqlHistoryRepository.cs
index c2834eed5..5dc0869dd 100644
--- a/src/EFCore.PG/Migrations/Internal/NpgsqlHistoryRepository.cs
+++ b/src/EFCore.PG/Migrations/Internal/NpgsqlHistoryRepository.cs
@@ -1,4 +1,5 @@
 using Npgsql.EntityFrameworkCore.PostgreSQL.Metadata.Conventions;
+using Npgsql.EntityFrameworkCore.PostgreSQL.Metadata.Internal;
 
 namespace Npgsql.EntityFrameworkCore.PostgreSQL.Migrations.Internal;
 
@@ -105,7 +106,16 @@ protected override IReadOnlyList<MigrationCommand> GetCreateCommands()
         var model = EnsureModel();
 
         var operations = Dependencies.ModelDiffer.GetDifferences(null, model.GetRelationalModel());
-        var commandList = Dependencies.MigrationsSqlGenerator.Generate(operations, model);
+
+        // Workaround for https://github.com/npgsql/efcore.pg/issues/3496: filter out extension-related operations.
+        // On managed PostgreSQL services (e.g. Azure Flexible Server), CREATE EXTENSION requires sometimes superuser privileges
+        // even with IF NOT EXISTS. Since extension creation isn't needed for the history table, we exclude these
+        // operations to avoid permission errors for non-superuser application accounts.
+        var operationsWithoutExtensions = operations
+            .Where(o => !o.GetAnnotations().Any(a => a.Name.StartsWith(NpgsqlAnnotationNames.PostgresExtensionPrefix, StringComparison.Ordinal)))
+            .ToList();
+
+        var commandList = Dependencies.MigrationsSqlGenerator.Generate(operationsWithoutExtensions, model);
         return commandList;
     }
 
diff --git a/test/EFCore.PG.Tests/Migrations/NpgsqlHistoryRepositoryTest.cs b/test/EFCore.PG.Tests/Migrations/NpgsqlHistoryRepositoryTest.cs
index 046271648..2df3a8aa2 100644
--- a/test/EFCore.PG.Tests/Migrations/NpgsqlHistoryRepositoryTest.cs
+++ b/test/EFCore.PG.Tests/Migrations/NpgsqlHistoryRepositoryTest.cs
@@ -77,6 +77,28 @@ IF NOT EXISTS(SELECT 1 FROM pg_namespace WHERE nspname = 'my') THEN
     CONSTRAINT "PK___EFMigrationsHistory" PRIMARY KEY ("MigrationId")
 );
 
+""", sql, ignoreLineEndingDifferences: true);
+    }
+
+    [ConditionalFact]
+    public void GetCreateIfNotExistsScript_works_with_schema_and_extension()
+    {
+        var sql = CreateHistoryRepositoryWithNetTopologySuite("my").GetCreateIfNotExistsScript();
+
+        Assert.Equal(
+            """
+DO $EF$
+BEGIN
+    IF NOT EXISTS(SELECT 1 FROM pg_namespace WHERE nspname = 'my') THEN
+        CREATE SCHEMA my;
+    END IF;
+END $EF$;
+CREATE TABLE IF NOT EXISTS my."__EFMigrationsHistory" (
+    "MigrationId" character varying(150) NOT NULL,
+    "ProductVersion" character varying(32) NOT NULL,
+    CONSTRAINT "PK___EFMigrationsHistory" PRIMARY KEY ("MigrationId")
+);
+
 """, sql, ignoreLineEndingDifferences: true);
     }
 
@@ -156,6 +178,19 @@ private static IHistoryRepository CreateHistoryRepository(string schema = null)
                     .Options)
             .GetService<IHistoryRepository>();
 
+    private static IHistoryRepository CreateHistoryRepositoryWithNetTopologySuite(string schema = null)
+        => new TestDbContext(
+                new DbContextOptionsBuilder()
+                    .UseInternalServiceProvider(
+                        NpgsqlTestHelpers.Instance.CreateServiceProvider(
+                            new ServiceCollection().AddEntityFrameworkNpgsqlNetTopologySuite()))
+                    .UseNpgsql(
+                        new NpgsqlConnection("Host=localhost;Database=DummyDatabase"),
+                        b => b.MigrationsHistoryTable(HistoryRepository.DefaultTableName, schema)
+                            .UseNetTopologySuite())
+                    .Options)
+            .GetService<IHistoryRepository>();
+
     private class TestDbContext(DbContextOptions options) : DbContext(options)
     {
         public DbSet<Blog> Blogs { get; set; }