diff --git a/doc/reference/autoinstall-reference.rst b/doc/reference/autoinstall-reference.rst
index cfea33846..9fdca7c5f 100644
--- a/doc/reference/autoinstall-reference.rst
+++ b/doc/reference/autoinstall-reference.rst
@@ -3,7 +3,11 @@
 Autoinstall configuration reference manual
 ==========================================
 
-The autoinstall file uses the YAML format. At the top level, it must be a mapping containing the keys described in this document. Unrecognised keys are ignored.
+The autoinstall file uses the YAML format. At the top level, it must be a
+mapping containing the keys described in this document. Unrecognised keys
+are ignored in version 1, but will cause a fatal validation error in future
+versions.
+
 
 .. _ai-schema:
 
@@ -25,6 +29,12 @@ Several configuration keys are lists of commands to be executed. Each command ca
 Top-level keys
 --------------
 
+
+.. warning::
+  In version 1, Subiquity will emit warnings when encountering unrecognised
+  keys. In later versions, a fatal validation error is thrown and the
+  installation will halt.
+
 .. _ai-version:
 
 version
diff --git a/subiquity/server/server.py b/subiquity/server/server.py
index cdee8ff0f..826005d9f 100644
--- a/subiquity/server/server.py
+++ b/subiquity/server/server.py
@@ -14,11 +14,12 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import asyncio
+import copy
 import logging
 import os
 import sys
 import time
-from typing import List, Optional
+from typing import Any, List, Optional
 
 import jsonschema
 import yaml
@@ -552,8 +553,97 @@ async def apply_autoinstall_config(self, context):
             await controller.apply_autoinstall_config()
             await controller.configured()
 
+    def filter_autoinstall(
+        self,
+        autoinstall_config: dict[str, Any],
+    ) -> tuple[dict[str, Any], dict[str, Any]]:
+        """Separates autoinstall config by known and uknown keys"""
+
+        invalid_config: dict[str, Any] = copy.deepcopy(autoinstall_config)
+
+        # Pop keys of all loaded controllers, if they exists
+        for controller in self.controllers.instances:
+            invalid_config.pop(controller.autoinstall_key, None)
+
+        # Pop server keys, if they exist
+        for key in self.base_schema["properties"]:
+            invalid_config.pop(key, None)
+
+        valid_config: dict[str, Any] = copy.deepcopy(autoinstall_config)
+
+        # Remove the keys we isolated
+        for key in invalid_config:
+            valid_config.pop(key)
+
+        return (valid_config, invalid_config)
+
+    @with_context(name="top_level_keys")
+    def _enforce_top_level_keys(
+        self,
+        *,
+        autoinstall_config: dict[str, Any],
+        context: Context,
+    ) -> dict[str, Any]:
+        """Enforces usage of known top-level keys.
+
+        In Autoinstall v1, unknown top-level keys are removed from
+        the config and a cleaned config is returned.
+
+        In Autoinstall v2, unknown top-level keys result in a fatal
+        AutoinstallValidationError
+
+        Only checks for unrecognized keys, doesn't validate them.
+        Requires a version number, so this should be called after
+        validating against the schema.
+
+        """
+
+        valid_config, invalid_config = self.filter_autoinstall(autoinstall_config)
+
+        # If no bad keys, return early
+        if len(invalid_config.keys()) == 0:
+            return autoinstall_config
+
+        # If the version is early enough, only warn
+        version: int = autoinstall_config["version"]
+
+        ctx = context
+        if version == 1:
+            # Warn then clean out bad keys and return
+
+            for key in invalid_config:
+                warning = f"Unrecognized top-level key {key!r}"
+                log.warning(warning)
+                ctx.warning(warning)
+
+            warning = (
+                "Unrecognized top-level keys will cause Autoinstall to "
+                "throw an error in future versions."
+            )
+            log.warning(warning)
+            ctx.warning(warning)
+
+            return valid_config
+
+        else:
+            for key in invalid_config:
+                error = f"Unrecognized top-level key {key!r}"
+                log.error(error)
+                ctx.error(error)
+
+            error = "Unrecognized top-level keys are unsupported"
+            log.error(error)
+            ctx.error(error)
+
+            raw_keys = (f"{key!r}" for key in invalid_config)
+            details: str = f"Unrecognized top-level key(s): {', '.join(raw_keys)}"
+            raise AutoinstallValidationError(
+                owner="top-level keys",
+                details=details,
+            )
+
     def validate_autoinstall(self):
-        with self.context.child("core_validation", level="INFO"):
+        with self.context.child("core_validation", level="INFO") as ctx:
             try:
                 jsonschema.validate(self.autoinstall_config, self.base_schema)
             except ValidationError as original_exception:
@@ -566,6 +656,12 @@ def validate_autoinstall(self):
 
                 raise new_exception from original_exception
 
+            # Enforce top level keys after ensuring we have a version number
+            self.autoinstall_config = self._enforce_top_level_keys(
+                autoinstall_config=self.autoinstall_config,
+                context=ctx,
+            )
+
     def load_autoinstall_config(self, *, only_early):
         log.debug(
             "load_autoinstall_config only_early %s file %s",
diff --git a/subiquity/server/tests/test_server.py b/subiquity/server/tests/test_server.py
index 292980f57..17d893176 100644
--- a/subiquity/server/tests/test_server.py
+++ b/subiquity/server/tests/test_server.py
@@ -13,8 +13,10 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+import copy
 import os
 import shlex
+from typing import Any
 from unittest.mock import AsyncMock, Mock, patch
 
 import jsonschema
@@ -125,7 +127,9 @@ def test_bogus_autoinstall_argument(self):
         with self.assertRaises(Exception):
             self.server.select_autoinstall()
 
-    def test_early_commands_changes_autoinstall(self):
+    # Only care about changes to autoinstall, not validity
+    @patch("subiquity.server.server.SubiquityServer.validate_autoinstall")
+    def test_early_commands_changes_autoinstall(self, validate_mock):
         self.server.controllers = Mock()
         self.server.controllers.instances = []
         rootpath = self.path(root_autoinstall_path)
@@ -166,6 +170,33 @@ async def asyncSetUp(self):
         }
         self.server.make_apport_report = Mock()
 
+    # Pseudo Load Controllers to avoid patching the loading logic for each
+    # controller when we still want access to class attributes
+    def pseudo_load_controllers(self):
+        controller_classes = []
+        for prefix in self.server.controllers.controller_names:
+            controller_classes.append(
+                self.server.controllers._get_controller_class(prefix)
+            )
+        self.server.controllers.instances = controller_classes
+
+    def load_config_and_controllers(
+        self, config: dict[str, Any]
+    ) -> tuple[dict[str, Any], dict[str, Any]]:
+        """Loads an autoinstall config and controllers.
+
+        Loads the provided autoinstall config and the controllers.
+        Returns the valid and invalid portions of the config.
+        """
+        # Reset base schema
+        self.server.base_schema = SubiquityServer.base_schema
+
+        self.server.autoinstall_config = config
+
+        self.pseudo_load_controllers()
+
+        return self.server.filter_autoinstall(config)
+
     def test_valid_schema(self):
         """Test that the expected autoinstall JSON schema is valid"""
 
@@ -232,6 +263,70 @@ async def test_autoinstall_validation__no_error_report(self):
         error = NonReportableError.from_exception(exception)
         self.assertEqual(error, self.server.nonreportable_error)
 
+    @patch("subiquity.server.server.log")
+    async def test_autoinstall_validation__strict_top_level_keys_warn(self, log_mock):
+        """Test strict top-level key enforcement warnings in v1"""
+
+        bad_ai_data = {
+            "version": 1,
+            "interactive-sections": ["identity"],
+            "apt": "Invalid but deferred",
+            "literally-anything": "lmao",
+        }
+
+        good, bad = self.load_config_and_controllers(bad_ai_data)
+
+        # OK in Version 1 but ensure warnings and stripped config
+        self.server.validate_autoinstall()
+        log_mock.warning.assert_called()
+        log_mock.error.assert_not_called()
+        self.assertEqual(self.server.autoinstall_config, good)
+
+    @patch("subiquity.server.server.log")
+    async def test_autoinstall_validation__strict_top_level_keys_error(self, log_mock):
+        """Test strict top-level key enforcement errors in v2 or greater"""
+
+        bad_ai_data = {
+            "version": 2,
+            "interactive-sections": ["identity"],
+            "apt": "Invalid but deferred",
+            "literally-anything": "lmao",
+        }
+
+        self.load_config_and_controllers(bad_ai_data)
+
+        # TODO: remove once V2 is enabled
+        self.server.base_schema["properties"]["version"]["maximum"] = 2
+
+        # Not OK in Version >= 2
+        with self.assertRaises(AutoinstallValidationError) as ctx:
+            self.server.validate_autoinstall()
+
+        self.assertIn("top-level keys", str(ctx.exception))
+
+        log_mock.error.assert_called()
+        log_mock.warning.assert_not_called()
+
+    async def test_autoinstall_validation__filter_autoinstall(self):
+        """Test autoinstall config filtering"""
+
+        # Mixed data: has base sections, controller section, and a bad key
+        autoinstall_config = {
+            "version": 1,  # stay
+            "interactive-sections": ["identity"],  # stay
+            "apt": "...",  # strip
+            "some-bad-key": "...",  # stay
+        }
+
+        self.server.base_schema = SubiquityServer.base_schema
+        self.pseudo_load_controllers()
+
+        valid, invalid = self.server.filter_autoinstall(autoinstall_config)
+
+        real_valid_keys = set(("version", "interactive-sections", "apt"))
+        self.assertEqual(set(valid.keys()), real_valid_keys)
+        self.assertEqual(set(invalid.keys()), set(("some-bad-key",)))
+
 
 class TestMetaController(SubiTestCase):
     async def test_interactive_sections_not_present(self):