diff --git a/.changeset/four-tips-peel.md b/.changeset/four-tips-peel.md
new file mode 100644
index 000000000..f56d5208a
--- /dev/null
+++ b/.changeset/four-tips-peel.md
@@ -0,0 +1,5 @@
+---
+'myst-config': patch
+---
+
+The options are immutable and we must clone the object.
diff --git a/packages/myst-config/src/site/validators.ts b/packages/myst-config/src/site/validators.ts
index 33018e0e5..3c188efb1 100644
--- a/packages/myst-config/src/site/validators.ts
+++ b/packages/myst-config/src/site/validators.ts
@@ -179,7 +179,7 @@ export function validateSiteConfig(input: any, opts: ValidationOptions) {
         opts.errorLogFn?.(`duplicate value for site option ${key}`);
       } else {
         opts.warningLogFn?.(`extra site options should be nested under "options" key: ${key}`);
-        (value.options ??= {})[key] = valueAsObject[key];
+        value.options = { ...value.options, [key]: valueAsObject[key] };
       }
     });
   return validateSiteConfigKeys(value, opts);