How to populate a sub-document in mongoose after creating it?

In order to populate referenced subdocuments, you need to explicitly define the document collection to which the ID references to (like created_by: { type: Schema.Types.ObjectId, ref: 'User' }).

Given this reference is defined and your schema is otherwise well defined as well, you can now just call populate as usual (e.g. populate('comments.created_by'))

Proof of concept code:

// Schema
var mongoose = require('mongoose');
var Schema = mongoose.Schema;

var UserSchema = new Schema({
  name: String
});

var CommentSchema = new Schema({
  text: String,
  created_by: { type: Schema.Types.ObjectId, ref: 'User' }
});

var ItemSchema = new Schema({
   comments: [CommentSchema]
});

// Connect to DB and instantiate models    
var db = mongoose.connect('enter your database here');
var User = db.model('User', UserSchema);
var Comment = db.model('Comment', CommentSchema);
var Item = db.model('Item', ItemSchema);

// Find and populate
Item.find({}).populate('comments.created_by').exec(function(err, items) {
    console.log(items[0].comments[0].created_by.name);
});

Finally note that populate works only for queries so you need to first pass your item into a query and then call it:

item.save(function(err, item) {
    Item.findOne(item).populate('comments.created_by').exec(function (err, item) {
        res.json({
            status: 'success',
            message: "You have commented on this item",
            comment: item.comments.id(comment._id)
        });
    });
});