Database
[{"_id":"5f969419d40c1580f2d4aa36","users":{"foo@bar.com":"baz","foo2@bar.com":"baz2"}},{"_id":"5f9694d4d40c1580f2d4aa38","users":{"baz@test.com":"foo"}}]
Query
db.collection.aggregate([{"$project":{"users":{"$objectToArray":"$users"}}},{"$match":{"users.k":"foo@bar.com"}},{$set:{users:{$filter:{input:"$users",cond:{$eq:["$$this.k","foo2@bar.com"]}}}}},{"$project":{"users":{"$arrayToObject":"$users"}}}])