How to build this query to update all items at once?

[steevej (Steeve Juneau)]

First please followup on

Indexes are not being used

It should. Share the explain plan.

Query taking long time to run

As mentioned You do not have You have a compoud index with createdAt as a secondary key.

Limit the items returned from array

The syntax findOne(…).lean().exec(), as I do not recognize it, makes me think that you might be using an obstruction abstraction layer like mongoose. If it is the case it might be a good idea to add mongoose in the tag list so that people only tracking mongoose related topics see your post. How does it behave exactly? Errors or wrong results? I am not sure you can have projection with exclusion like lastRefreshed:0 and inclusion like the tokens specification. As mentioned by @Prasad_Saya, …

How can I get only a specific array inside array of subdocuments?

As already mentioned in your other threads: And the link to $filter was already provided in one of your other threads: You need to aggregate starting with a $match stage that has the same query as your findOne(). You then need a $project stage that $filter the entries array using the username in the condition.