diff --git a/fastappkit/cli/migrate.py b/fastappkit/cli/migrate.py
index 0f71e55..d73f6a4 100644
--- a/fastappkit/cli/migrate.py
+++ b/fastappkit/cli/migrate.py
@@ -70,6 +70,10 @@ def core(
         if str(project_root) not in sys.path:
             sys.path.insert(0, str(project_root))
 
+        # Load registry to identify external apps (needed to exclude their tables from autogenerate)
+        loader = AppLoader(project_root)
+        registry = loader.load_all()
+
         # Try to collect metadata from core module for core migrations
         metadata_collector = MetadataCollector()
         # Try to collect from core.models only
@@ -96,6 +100,7 @@ def core(
             message,
             core_migration_path,
             target_metadata=core_metadata_obj,
+            registry=registry,  # Pass registry so external app tables can be excluded
         )
         typer.echo(f"✅ Created migration: {migration_path}")
     except Exception as e:
diff --git a/fastappkit/cli/templates/app/external/README.md.j2 b/fastappkit/cli/templates/app/external/README.md.j2
index 9830e88..312ac26 100644
--- a/fastappkit/cli/templates/app/external/README.md.j2
+++ b/fastappkit/cli/templates/app/external/README.md.j2
@@ -112,9 +112,12 @@ alembic downgrade -1
 alembic upgrade head --sql
 ```
 
-**Database URL**: The `DATABASE_URL` is read from the `.env` file automatically. You can also:
-- Set `DATABASE_URL` environment variable (takes precedence)
-- Edit `alembic.ini` sqlalchemy.url (fallback)
+**Database URL**: The database URL is determined in this order:
+1. App's Settings class (loads from `.env` file) - **RECOMMENDED**
+2. `DATABASE_URL` environment variable
+3. `alembic.ini` sqlalchemy.url (fallback only)
+
+The app's `Settings` class automatically loads from `.env` file, so just configure your `.env` file and it will be used.
 
 ### When Using the External App in a Core Project
 
diff --git a/fastappkit/cli/templates/app/external/alembic.ini.j2 b/fastappkit/cli/templates/app/external/alembic.ini.j2
index e444566..06d381b 100644
--- a/fastappkit/cli/templates/app/external/alembic.ini.j2
+++ b/fastappkit/cli/templates/app/external/alembic.ini.j2
@@ -61,15 +61,16 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 
 # Database URL configuration
 #
-# This can be configured in three ways (in order of precedence):
-# 1. DATABASE_URL environment variable (from .env file when running independently)
-# 2. This sqlalchemy.url setting (fallback)
-# 3. Set programmatically in migrations/env.py
+# IMPORTANT: The database URL is determined in this order (when running independently):
+# 1. App's Settings class (loads from .env file) - RECOMMENDED
+# 2. DATABASE_URL environment variable
+# 3. This sqlalchemy.url setting (fallback only)
 #
 # For independent development, create a .env file with:
 #   DATABASE_URL=sqlite:///./{{ app_name }}.db
 #
-# The migrations/env.py will automatically read DATABASE_URL from the environment.
+# The migrations/env.py will automatically use Settings to load from .env file.
+# This sqlalchemy.url is only used as a last resort fallback.
 # Default uses SQLite for development
 sqlalchemy.url = sqlite:///./{{ app_name }}.db
 
diff --git a/fastappkit/cli/templates/app/external/config.py.j2 b/fastappkit/cli/templates/app/external/config.py.j2
index e7c0302..a79a4f5 100644
--- a/fastappkit/cli/templates/app/external/config.py.j2
+++ b/fastappkit/cli/templates/app/external/config.py.j2
@@ -15,17 +15,9 @@ class Settings(BaseSettings):
     Loads from .env file automatically.
     """
 
-    database_url: str = Field(
-        default="sqlite:///./{{ app_name }}.db",
-        alias="DATABASE_URL"
-    )
-    debug: bool = Field(
-        default=False,
-        alias="DEBUG"
-    )
+    database_url: str = Field(default="sqlite:///./{{ app_name }}.db")
+    debug: bool = Field(default=False)
 
     model_config = SettingsConfigDict(
-        env_file=".env",
-        env_file_encoding="utf-8",
-        populate_by_name=True
+        env_file=".env", env_file_encoding="utf-8", populate_by_name=True
     )
diff --git a/fastappkit/cli/templates/app/external/main.py.j2 b/fastappkit/cli/templates/app/external/main.py.j2
index 065eded..ee05e16 100644
--- a/fastappkit/cli/templates/app/external/main.py.j2
+++ b/fastappkit/cli/templates/app/external/main.py.j2
@@ -16,10 +16,10 @@ _current_dir = Path(__file__).parent
 if str(_current_dir) not in sys.path:
     sys.path.insert(0, str(_current_dir))
 
-from fastapi import FastAPI
+from fastapi import FastAPI  # noqa: E402
 
-from {{ app_name }}.config import Settings
-from {{ app_name }} import register
+from {{ app_name }}.config import Settings  # noqa: E402
+from {{ app_name }} import register  # noqa: E402
 
 # Load settings from .env
 settings = Settings()
@@ -41,4 +41,4 @@ if router is not None:
 if __name__ == "__main__":
     import uvicorn
 
-    uvicorn.run(app, host="127.0.0.1", port=8000, reload=True)
+    uvicorn.run("main:app", host="127.0.0.1", port=8000, reload=True)
diff --git a/fastappkit/cli/templates/app/external/migrations/env.py.j2 b/fastappkit/cli/templates/app/external/migrations/env.py.j2
index 727ef6b..b3f68c4 100644
--- a/fastappkit/cli/templates/app/external/migrations/env.py.j2
+++ b/fastappkit/cli/templates/app/external/migrations/env.py.j2
@@ -32,21 +32,41 @@ target_metadata = Base.metadata
 config = context.config
 
 # Get database URL with the following precedence order:
-# 1. Config (set by fastappkit when running from core project)
-# 2. DATABASE_URL environment variable (from .env file when running independently)
-# 3. alembic.ini sqlalchemy.url (fallback)
+# 1. Config (set by fastappkit when running from core project - config_file_name is None)
+# 2. App's Settings class (loads from .env file when running independently)
+# 3. DATABASE_URL environment variable (direct fallback)
+# 4. alembic.ini sqlalchemy.url (last resort)
 #
 # This allows the external app to work both:
-# - When used in a core project (fastappkit sets it via config)
-# - When developed independently (reads from .env file)
-database_url = config.get_main_option("sqlalchemy.url")
-if not database_url:
-    # If not set in config, try environment variable (from .env)
-    import os
-    database_url = os.getenv("DATABASE_URL")
-    if database_url:
-        config.set_main_option("sqlalchemy.url", database_url)
-# If still not set, alembic.ini's sqlalchemy.url will be used by Alembic
+# - When used in a core project (fastappkit sets it via config, config_file_name is None)
+# - When developed independently (reads from .env file via Settings, config_file_name is set)
+database_url = None
+
+# Check if fastappkit is running this (config_file_name is None when fastappkit runs it)
+# In that case, database URL is already set by fastappkit in config
+if config.config_file_name is None:
+    # Running from core project via fastappkit - use URL already set in config
+    database_url = config.get_main_option("sqlalchemy.url")
+else:
+    # Running independently - prioritize Settings/.env over alembic.ini
+    try:
+        from {{ app_name }}.config import Settings
+        settings = Settings()
+        database_url = settings.database_url
+    except (ImportError, AttributeError):
+        # Settings not available, try environment variable directly
+        import os
+        database_url = os.getenv("DATABASE_URL")
+
+    # If still not set, alembic.ini's sqlalchemy.url will be used by Alembic
+    if not database_url:
+        database_url = config.get_main_option("sqlalchemy.url")
+
+# Strip async drivers (e.g., +asyncpg, +aiosqlite) since Alembic doesn't support async
+if database_url:
+    for async_driver in ["+asyncpg", "+aiosqlite", "+asyncmy"]:
+        database_url = database_url.replace(async_driver, "")
+    config.set_main_option("sqlalchemy.url", database_url)
 
 # Interpret the config file for Python logging
 if config.config_file_name is not None:
diff --git a/fastappkit/cli/templates/app/internal/migrations/env.py.j2 b/fastappkit/cli/templates/app/internal/migrations/env.py.j2
index 0b22f68..54700bd 100644
--- a/fastappkit/cli/templates/app/internal/migrations/env.py.j2
+++ b/fastappkit/cli/templates/app/internal/migrations/env.py.j2
@@ -20,7 +20,7 @@ if str(_project_root) not in sys.path:
     sys.path.insert(0, str(_project_root))
 
 # Import core settings
-from core.config import Settings
+from core.config import Settings  # noqa: E402
 
 # Get settings
 settings = Settings()
diff --git a/fastappkit/cli/templates/project/core/config.py.j2 b/fastappkit/cli/templates/project/core/config.py.j2
index c68e7fb..e211619 100644
--- a/fastappkit/cli/templates/project/core/config.py.j2
+++ b/fastappkit/cli/templates/project/core/config.py.j2
@@ -15,17 +15,9 @@ class Settings(BaseSettings):
     Loads from .env file automatically.
     """
 
-    database_url: str = Field(
-        default="sqlite:///./{{ project_name }}.db",
-        alias="DATABASE_URL"
-    )
-    debug: bool = Field(
-        default=False,
-        alias="DEBUG"
-    )
+    database_url: str = Field(default="sqlite:///./{{ app_name }}.db")
+    debug: bool = Field(default=False)
 
     model_config = SettingsConfigDict(
-        env_file=".env",
-        env_file_encoding="utf-8",
-        populate_by_name=True
+        env_file=".env", env_file_encoding="utf-8", populate_by_name=True
     )
diff --git a/fastappkit/cli/templates/project/core/db/migrations/env.py.j2 b/fastappkit/cli/templates/project/core/db/migrations/env.py.j2
index 0c10bd7..73c30c7 100644
--- a/fastappkit/cli/templates/project/core/db/migrations/env.py.j2
+++ b/fastappkit/cli/templates/project/core/db/migrations/env.py.j2
@@ -18,8 +18,8 @@ if str(_project_root) not in sys.path:
     sys.path.insert(0, str(_project_root))
 
 # Import your settings
-from core.config import Settings
-from sqlalchemy import MetaData
+from core.config import Settings  # noqa: E402
+from sqlalchemy import MetaData  # noqa: E402
 
 # Get settings
 settings = Settings()
@@ -37,6 +37,27 @@ if target_metadata is None:
         # No core models yet, use empty MetaData for initial migration
         target_metadata = MetaData()
 
+# Get external app tables to exclude from autogenerate (set by fastappkit)
+# This prevents core migrations from dropping external app tables
+exclude_external_app_tables = config.attributes.get("exclude_external_app_tables", set())
+
+
+def include_object(object, name, type_, reflected, compare_to):
+    """
+    Filter objects during autogenerate to exclude external app tables.
+
+    This ensures core migrations don't try to drop tables that belong to external apps,
+    which manage their own migrations independently.
+    """
+    if type_ == "table":
+        # Exclude external app tables and version tables
+        if name in exclude_external_app_tables:
+            return False
+        # Also exclude external app version tables (alembic_version_<appname>)
+        if name.startswith("alembic_version_") and name != "alembic_version":
+            return False
+    return True
+
 # Set database URL from settings
 # Strip async drivers (e.g., +asyncpg, +aiosqlite) since Alembic doesn't support async
 database_url = settings.database_url
@@ -61,6 +82,7 @@ def run_migrations_offline() -> None:
         target_metadata=target_metadata,
         literal_binds=True,
         dialect_opts={"paramstyle": "named"},
+        include_object=include_object,
     )
 
     with context.begin_transaction():
@@ -76,7 +98,11 @@ def run_migrations_online() -> None:
     )
 
     with connectable.connect() as connection:
-        context.configure(connection=connection, target_metadata=target_metadata)
+        context.configure(
+            connection=connection,
+            target_metadata=target_metadata,
+            include_object=include_object,
+        )
 
         with context.begin_transaction():
             context.run_migrations()
diff --git a/fastappkit/cli/templates/project/core/models.py.j2 b/fastappkit/cli/templates/project/core/models.py.j2
index ce2d646..ae577e1 100644
--- a/fastappkit/cli/templates/project/core/models.py.j2
+++ b/fastappkit/cli/templates/project/core/models.py.j2
@@ -35,4 +35,4 @@ class Base(DeclarativeBase):
 #
 #     id = Column(Integer, primary_key=True, index=True)
 #     name = Column(String, nullable=False)
-#     created_at = Column(DateTime, default=datetime.utcnow)
+#     created_at = Column(DateTime, default=datetime.now(timezone.utc))
diff --git a/fastappkit/migrations/autogen.py b/fastappkit/migrations/autogen.py
index 09c34b0..44d47a6 100644
--- a/fastappkit/migrations/autogen.py
+++ b/fastappkit/migrations/autogen.py
@@ -14,6 +14,7 @@
 from fastappkit.core.registry import AppMetadata
 from fastappkit.core.types import AppType
 from fastappkit.migrations.context import MigrationContextBuilder
+from fastappkit.migrations.version import VersionTableManager
 
 if TYPE_CHECKING:
     from fastappkit.core.registry import AppRegistry
@@ -79,17 +80,43 @@ def generate(
                 # External app or no registry - use only app's metadata
                 target_metadata = self.metadata_collector.collect_metadata(app_metadata)
 
+        # For core and internal app migrations (they share the same migration directory),
+        # collect external app table names to exclude from autogenerate
+        # This prevents core/internal migrations from dropping external app tables
+        external_app_tables: set[str] = set()
+        # Core and internal apps both use core/db/migrations/ and share alembic_version table
+        # So they both need to exclude external app tables
+        if app_metadata.app_type == AppType.INTERNAL and registry:
+            # Collect all external app tables and version tables
+            for ext_app in registry.get_by_type(AppType.EXTERNAL):
+                # Get external app version table
+                version_table = VersionTableManager.get_version_table(
+                    AppType.EXTERNAL, ext_app.name
+                )
+                external_app_tables.add(version_table)
+
+                # Get external app model tables
+                ext_metadata = self.metadata_collector.collect_metadata(ext_app)
+                if ext_metadata:
+                    for table_name in ext_metadata.tables.keys():
+                        external_app_tables.add(table_name)
+
         # Build Alembic config
         # For internal apps, migration_path is core/db/migrations (no special handling needed)
         alembic_cfg = self.context_builder.build_alembic_config(
             app_metadata,
             migration_path,
+            registry=registry,
         )
 
         # Set target metadata in config (for autogenerate)
         if target_metadata:
             alembic_cfg.attributes["target_metadata"] = target_metadata
 
+        # Set external app tables to exclude (for core migrations only)
+        if external_app_tables:
+            alembic_cfg.attributes["exclude_external_app_tables"] = external_app_tables
+
         # Generate migration
         try:
             # Alembic revision command doesn't return path directly