Firestore doesn't support JavaScript objects with custom prototypes?

The firestore Node.js client do not support serialization of custom classes.

You will find more explanation in this issue:
https://github.com/googleapis/nodejs-firestore/issues/143
"We explicitly decided to not support serialization of custom classes for the Web and Node.JS client"

A solution is to convert the nested object to a plain object. For example by using lodash or JSON.stringify.

firestore.collection('collectionName')
    .doc('id')
    .set(JSON.parse(JSON.stringify(myCustomObject)));

Here is a related post:
Firestore: Add Custom Object to db

Another way is less resources consuming:

firestore
  .collection('collectionName')
  .doc('id')
  .set(Object.assign({}, myCustomObject));

Note: it works only for objects without nested objects.

Also you may use class-transformer and it's classToPlain() along with exposeUnsetFields option to omit undefined values.

npm install class-transformer
or
yarn add class-transformer

import {classToPlain} from 'class-transformer';

firestore
  .collection('collectionName')
  .doc('id')
  .set(classToPlain(myCustomObject, {exposeUnsetFields: false}));