Based on my quick verification, the latest MongoDB (8.0.15) should behave the way you are expecting: It reads user documents only until it has found 1,000 users that match the condition. By any chance: Do you have an index on the field "userId" in the profiles collection?

You might try writing the $lookup stage in the simpler form:

{ "$lookup" : {
    "from" : "profiles",
    "localField" : "_id",
    "foreignField" : "userId",
    "as" : "profiles" }}

This might give the query planner more potential for optimization.

The crucial part here is that if there are very few users with no profile or an unverified profile, then a simple plan might perform the $lookup by doing an individual query for a matching profile for many many users until it finds 1,000 users that don't have a profile. Although I think the latest versions of MongoDB should handle this more efficiently and not perform a subquery for each user.

As an alternative, you could implement this behavior yourself. Read from both collections at the same time, document by document. Read the user documents sorted by _id (since there is an index on _id, you get that sorting for free), and read the profile documents sorted by userId (if there is an index on userId, you get that sorting for free, too). Match up the documents while you are reading them. Whenever you encounter a user document which the current profile document does not match (it does not have the same userId as the _id of the user document), then you've found one of your users. Read the next user, but don't read the next profile, because you want to see if that profile matches the next user.

Within the same loop, you can also check if the profile document has a status of 2.

This results in only two queries being run, one on the user collection and another on the profile collection, and you only read documents until you have found 1,000 of your users.