diff --git a/apps/oxlint/src-js/plugins/load.ts b/apps/oxlint/src-js/plugins/load.ts
index 6b64d11dd2b42..99a1271df8417 100644
--- a/apps/oxlint/src-js/plugins/load.ts
+++ b/apps/oxlint/src-js/plugins/load.ts
@@ -167,6 +167,9 @@ export function registerPlugin(plugin: Plugin, packageName: string | null): Plug
         if (!isArray(inputDefaultOptions)) {
           throw new TypeError("`rule.meta.defaultOptions` must be an array if provided");
         }
+        // TODO: This isn't quite safe, as `defaultOptions` isn't from JSON, and `deepFreezeJsonArray`
+        // assumes it is. We should perform options merging on Rust side instead, and also validate
+        // `defaultOptions` against options schema.
         deepFreezeJsonArray(inputDefaultOptions);
         defaultOptions = inputDefaultOptions;
       }
diff --git a/apps/oxlint/src-js/plugins/options.ts b/apps/oxlint/src-js/plugins/options.ts
index 98912cf699c1f..3a7516eac74ec 100644
--- a/apps/oxlint/src-js/plugins/options.ts
+++ b/apps/oxlint/src-js/plugins/options.ts
@@ -174,9 +174,19 @@ function mergeValues(configValue: JsonValue, defaultValue: JsonValue): JsonValue
   const merged = { ...defaultValue, ...configValue };
 
   // Symbol properties are not possible in JSON, so no need to handle them here.
-  // All properties are enumerable own properties, so can use simple `for..in` loop.
-  for (const key in configValue) {
-    if (key in defaultValue) {
+  //
+  // `defaultValue` is not from JSON, so we can't use a simple `for..in` loop over `defaultValue`.
+  // That would also pick up enumerable properties from prototype of `defaultValue`.
+  // `configValue` *is* from JSON, so simple `key in configValue` check is fine.
+  //
+  // A malicious plugin could potentially get up to mischief here (prototype pollution?) if `defaultValue` is a `Proxy`.
+  // But plugins are executable code, so they have far easier ways to do that. No point in defending against it here.
+  for (const key of Object.keys(defaultValue)) {
+    if (key in configValue) {
+      // `key` is an own property of both `configValue` and `defaultValue`, so must be an own property of `merged` too.
+      // Therefore, we don't need special handling for if `key` is `"__proto__"`.
+      // All the property reads and writes here will affect only the owned properties of these objects,
+      // (including if those properties are named `"__proto__"`).
       merged[key] = mergeValues(configValue[key], defaultValue[key]);
     } else {
       deepFreezeValue(configValue[key]);