diff --git a/datasette/app.py b/datasette/app.py
index 2df6e4e8..f0349895 100644
--- a/datasette/app.py
+++ b/datasette/app.py
@@ -696,6 +696,8 @@ class Datasette:
             env=self._jinja_env, datasette=self
         ):
             await await_me_maybe(hook)
+        # Ensure internal tables and metadata are populated before startup hooks
+        await self._refresh_schemas()
         for hook in pm.hook.startup(datasette=self):
             await await_me_maybe(hook)
         self._startup_invoked = True
diff --git a/datasette/cli.py b/datasette/cli.py
index db777fe8..32a4d898 100644
--- a/datasette/cli.py
+++ b/datasette/cli.py
@@ -661,15 +661,16 @@ def serve(
         # Private utility mechanism for writing unit tests
         return ds
 
+    # Run async soundness checks before startup hooks, since invoke_startup
+    # now populates internal tables which requires querying each database
+    run_sync(lambda: check_databases(ds))
+
     # Run the "startup" plugin hooks
     try:
         run_sync(ds.invoke_startup)
     except StartupError as e:
         raise click.ClickException(e.args[0])
 
-    # Run async soundness checks - but only if we're not under pytest
-    run_sync(lambda: check_databases(ds))
-
     if headers and not get:
         raise click.ClickException("--headers can only be used with --get")
 
diff --git a/tests/plugins/my_plugin_2.py b/tests/plugins/my_plugin_2.py
index 35775ef9..9e8d9b2b 100644
--- a/tests/plugins/my_plugin_2.py
+++ b/tests/plugins/my_plugin_2.py
@@ -127,6 +127,18 @@ def startup(datasette):
         internal_db = datasette.get_internal_database()
         result = await internal_db.execute("select 1 + 1")
         datasette._startup_hook_calculation = result.first()[0]
+        # Check that metadata tables have been populated before startup fires
+        metadata_rows = await internal_db.execute(
+            "select key, value from metadata_instance"
+        )
+        datasette._startup_metadata_keys = [row["key"] for row in metadata_rows]
+        # Check that catalog/schema tables have been populated before startup fires
+        catalog_rows = await internal_db.execute(
+            "select database_name from catalog_databases"
+        )
+        datasette._startup_catalog_databases = [
+            row["database_name"] for row in catalog_rows
+        ]
 
     return inner
 
diff --git a/tests/test_plugins.py b/tests/test_plugins.py
index fa9d1a1f..f2a47ab4 100644
--- a/tests/test_plugins.py
+++ b/tests/test_plugins.py
@@ -862,6 +862,18 @@ async def test_hook_startup(ds_client):
     assert 2 == ds_client.ds._startup_hook_calculation
 
 
+@pytest.mark.asyncio
+async def test_hook_startup_metadata_available(ds_client):
+    # Metadata from metadata.yaml should be populated before startup() fires
+    assert "title" in ds_client.ds._startup_metadata_keys
+
+
+@pytest.mark.asyncio
+async def test_hook_startup_catalog_populated(ds_client):
+    # Internal catalog tables should be populated before startup() fires
+    assert "fixtures" in ds_client.ds._startup_catalog_databases
+
+
 @pytest.mark.asyncio
 async def test_hook_canned_queries(ds_client):
     queries = (await ds_client.get("/fixtures.json")).json()["queries"]
diff --git a/tests/test_tracer.py b/tests/test_tracer.py
index 1e0d7001..6cc80fc4 100644
--- a/tests/test_tracer.py
+++ b/tests/test_tracer.py
@@ -32,25 +32,11 @@ def test_trace(trace_debug):
         assert isinstance(trace.get("params"), (list, dict, None.__class__))
 
     sqls = [trace["sql"] for trace in traces if "sql" in trace]
-    # There should be a mix of different types of SQL statement
-    expected = (
-        "CREATE TABLE ",
-        "PRAGMA ",
-        "INSERT OR REPLACE INTO ",
-        "INSERT INTO",
-        "select ",
-    )
-    for prefix in expected:
-        assert any(
-            sql.startswith(prefix) for sql in sqls
-        ), "No trace beginning with: {}".format(prefix)
-
-    # Should be at least one executescript
-    assert any(trace for trace in traces if trace.get("executescript"))
-    # And at least one executemany
-    execute_manys = [trace for trace in traces if trace.get("executemany")]
-    assert execute_manys
-    assert all(isinstance(trace["count"], int) for trace in execute_manys)
+    # There should be SQL statements from request handling in the trace.
+    # Note: CREATE TABLE, INSERT OR REPLACE, executescript, and executemany
+    # are not expected here because internal tables are now created and
+    # populated during invoke_startup(), before the request is traced.
+    assert any(sql.startswith("select ") for sql in sqls), "No select statements traced"
 
 
 def test_trace_silently_fails_for_large_page():