Database
db={"Collection1":[{"_id":"61cf8452fca008360872c9cd","name":"Aff 2"},{"_id":"61cf845ffca008360872c9d0","name":"AFF 1"},{"_id":"61cf8468fca008360872c9d3","name":"Aff 3"}],"Collection2":[{"_id":"61e05bb5fe1d8327d4c73663","userID":"61cf82dac828bd519cfd38ca","col_1_ID":"61cf845ffca008360872c9d0"},{"_id":"61e05c14fe1d8327d4c7367d","userID":"61cf82dac828bd519cfd38ca","col_1_ID":"61cf8468fca008360872c9d3"},{"_id":"61e05ca0fe1d8327d4c73695","userID":"61e05906246ccc41d4ebd30f","col_1_ID":"61cf8452fca008360872c9cd"},{"_id":"61e05c14fe1d8327d4c73600","userID":"61cf82dac828bd519cfd3111","col_1_ID":"61cf8468fca008360872c9d3"},]}
Query
db.Collection1.aggregate([{"$lookup":{"from":"Collection2","localField":"_id","foreignField":"col_1_ID","as":"joined_docs"}},{$unwind:{"path":"$joined_docs"}},{$group:{_id:{account_id:"$_id",account_name:"$name",},user_ids:{$push:{"userID":"$joined_docs.userID"}}}},{$match:{"user_ids.userID":{$nin:["61cf82dac828bd519cfd38ca"]}}},{$project:{user_ids:0}}])