diff --git a/packages/block-library/src/footnotes/index.js b/packages/block-library/src/footnotes/index.js
index c0f3d60ada5432..db9782cb567677 100644
--- a/packages/block-library/src/footnotes/index.js
+++ b/packages/block-library/src/footnotes/index.js
@@ -21,9 +21,8 @@ export const settings = {
 	edit,
 };
 
-// Would be good to remove the format and HoR if the block is unregistered.
-registerFormatType( formatName, format );
-
 export const init = () => {
+	// Would be good to remove the format if the block is unregistered.
+	registerFormatType( formatName, format );
 	initBlock( { name, metadata, settings } );
 };
diff --git a/packages/edit-site/src/index.js b/packages/edit-site/src/index.js
index ea2899a8abc105..818c8285933a02 100644
--- a/packages/edit-site/src/index.js
+++ b/packages/edit-site/src/index.js
@@ -29,6 +29,8 @@ import './hooks';
 import { store as editSiteStore } from './store';
 import App from './components/app';
 
+const DISALLOWED_BLOCKS = [ 'core/freeform', 'core/footnotes' ];
+
 /**
  * Initializes the site editor screen.
  *
@@ -45,7 +47,7 @@ export function initializeEditor( id, settings ) {
 
 	dispatch( blocksStore ).__experimentalReapplyBlockTypeFilters();
 	const coreBlocks = __experimentalGetCoreBlocks().filter(
-		( { name } ) => name !== 'core/freeform'
+		( { name } ) => ! DISALLOWED_BLOCKS.includes( name )
 	);
 	registerCoreBlocks( coreBlocks );
 	dispatch( blocksStore ).setFreeformFallbackBlockName( 'core/html' );
diff --git a/test/integration/helpers/integration-test-editor.js b/test/integration/helpers/integration-test-editor.js
index 6b954a895a51ac..7d5b3d9120509c 100644
--- a/test/integration/helpers/integration-test-editor.js
+++ b/test/integration/helpers/integration-test-editor.js
@@ -26,6 +26,8 @@ import {
 	unregisterBlockType,
 	getBlockTypes,
 } from '@wordpress/blocks';
+import { store as richTextStore } from '@wordpress/rich-text';
+import { useSelect, useDispatch } from '@wordpress/data';
 
 /**
  * Internal dependencies
@@ -60,13 +62,22 @@ export async function selectBlock( name ) {
 export function Editor( { testBlocks, settings = {} } ) {
 	const [ currentBlocks, updateBlocks ] = useState( testBlocks );
 
+	// Some blocks may register formats, eg. core/footnotes, so we need to also
+	// unregister those formats along with core blocks when the test is complete.
+	const availableFormats = useSelect(
+		( select ) => select( richTextStore ).getFormatTypes(),
+		[]
+	);
+	const { removeFormatTypes } = useDispatch( richTextStore );
+
 	useEffect( () => {
 		return () => {
-			getBlockTypes().forEach( ( { name } ) =>
-				unregisterBlockType( name )
-			);
+			getBlockTypes().forEach( ( { name } ) => {
+				unregisterBlockType( name );
+			} );
+			removeFormatTypes( availableFormats.map( ( { name } ) => name ) );
 		};
-	}, [] );
+	}, [ availableFormats, removeFormatTypes ] );
 
 	return (
 		<ShortcutProvider>