db={"products":[{"_id":"5dd5a66e8ddbd07fa251b88e","name":"Product One","internals":[{"default":false,"_id":"5e94da0f4d499253049ec532","name":"Type A"},{"_id":"5e94da0f4d499253049ec534","name":"Type B"},{"_id":"5e94da0f4d499253049ec536","name":"Type C"},{"_id":"5e94da0f4d499253049ec538","name":"Type D"},{"_id":"5f05d9a2bfc8fa1361d8beea","name":"Type E"},{"_id":"5f05d9a2bfc8fa1361d8beec","name":"Type F"}]},{"_id":"5e8b40bc91dd0e12e0219578","name":"Product Two","internals":[{"_id":"5e8b40bc91dd0e12e0219579","name":"Default Type"}],}],"users":[{"_id":"603d4c44505a51001c9b936f","email":"mister.paper@papers.org","name":"Mister Paper","profile":{"products":[{"_id":"603d4d101c24a9001cf79db1","product":"5dd5a66e8ddbd07fa251b88e","profile":"5e94da0f4d499253049ec534"},{"_id":"603fe3ebca063ea357ca0666","product":"5e8b40bc91dd0e12e0219578","profile":"5e8b40bc91dd0e12e0219579"},{"_id":"603fe3ebca063ea357ca0667","product":"5dd5a66e8ddbd07fa251b88e","profile":"5e94da0f4d499253049ec538"}],},"username":"mister.paper@papers.org"}]}

db.users.aggregate([/** sort it by latest (your requirement)*/{$sort:{created_at:-1}},/** unwind profile products*/{$unwind:"$profile.products"},/** lookup and populate product data* (only single product per document)*/{"$lookup":{from:"products",localField:"profile.products.product",foreignField:"_id",as:"products"}},/** unwind lookedup product data to take out* product object from array* one can also use "$arrayElemAt" as well for this*/{$unwind:"$products"},/** filter out your product internals*/{"$addFields":{"products.internals":{$filter:{input:"$products.internals",as:"internal",cond:{$eq:["$$internal._id","$profile.products.profile"]},}}}}])