If you are using Waterline or other database abstractions, my advice is to run the query natively in mongo.

This is how I would fix this in Sails.js (running Waterline):

let someQuery = {name: 'John Doe'}; 

MyModel.native(function (err, collection){
  collection.update(
    {query: someQuery},                   // Which documents to update?
    {$set:{field1: "value", foo:"bar"}},  // Our new values
    {multi: true},                        // To support update of multiple fields
    function(err, result){
      if (err) console.log(err)
      else console.log(result.result)
    })
});

updatedAt field is updated when you use update query of mongoose. if we directly use $set query it will only update the mentioned fields inside $ set query. The reason is updatedAt field is managed by mongoose not by mongodb.

If you are using mongoose, then relatively new feature (2020) gives you the option to override setting timestamps (or just one) on transactions.

Refer to docs

Example from docs shown below

const userSchema = mongoose.Schema({
  email: String
}, { timestamps: true });

const User = mongoose.model('User', userSchema);

const doc = await User.findOneAndUpdate({email: 'test@google.com'}, {email:'newtest@google.com'}, 
{new:true, upsert: true, timestamps:false});