diff --git a/packages/myst-cli/src/upgrade/toc.ts b/packages/myst-cli/src/upgrade/toc.ts
index 23676a190..51d70d184 100644
--- a/packages/myst-cli/src/upgrade/toc.ts
+++ b/packages/myst-cli/src/upgrade/toc.ts
@@ -229,5 +229,7 @@ function convertGeneric(dir: string, data: Record<string, unknown>): any {
   }
 }
 export function upgradeTOC(data: SphinxExternalTOC) {
-  return convertGeneric(cwd(), data) as any[];
+  const dir = cwd();
+  const entries = convertGeneric(dir, data) as any[];
+  return [{ file: relative(dir, resolveExtension(join(dir, data.root))!) }, ...entries];
 }
diff --git a/packages/myst-cli/src/upgrade/upgrade.ts b/packages/myst-cli/src/upgrade/upgrade.ts
index e646b39a1..a7112a2f2 100644
--- a/packages/myst-cli/src/upgrade/upgrade.ts
+++ b/packages/myst-cli/src/upgrade/upgrade.ts
@@ -16,6 +16,7 @@ export async function upgrade(session: ISession, opts: any) {
 
   const config: Config = {
     version: 1,
+    project: {}
   };
 
   // Does config file exist?
@@ -32,7 +33,7 @@ export async function upgrade(session: ISession, opts: any) {
     const content = fs.readFileSync('_toc.yml').toString();
     const data = validateSphinxExternalTOC(yaml.load(content));
     if (defined(data)) {
-      (config as any).toc = upgradeTOC(data);
+      (config as any).project.toc = upgradeTOC(data);
     }
   }