db={"Collection1":[{id:123,name:"xyz"},{id:234,name:"abc"},{id:345,name:"pqr"}],"Collection2":[{id:123,status:"y"},{id:789,status:"n"},{id:345,status:"y"}]}

db.Collection1.aggregate([{"$lookup":{"from":"Collection2","let":{"sourceId":"$id"},"pipeline":[{"$match":{"$expr":{"$eq":["$id","$$sourceId"]}}},{"$project":{"id":1,}},],"as":"foundCol2Docs"}},{"$match":{"foundCol2Docs":[],}},{"$unset":["foundCol2Docs"]},])