Database

db={"companies":[{"_id":"5dg8aa8c435b1e2868c841f6","name":"My Corp","externalId":"d7f348c9-c69b-69c4-923c-91458c53dc22","professionals_customers":[{"company":"6f4d01eb3b948150c2aad9c0"},{"company":"5dg7aa8c366b1e2868c841f6","contact":"5df8ab5c355b1e2999c841f7"},{"company":"5dg7aa8c366b1e2868c84111","contact":"5df8ab5c355b1e2999c841f7"}]},{"_id":"5dg8aa8c435b1e2868c84111","name":"My Corp 2","externalId":"d7f348c9-c69b-69c4-923c-91458c53dc11","professionals_customers":[{"company":"6f4d01eb3b948150c2aad9c1"},{"company":"5dg7aa8c366b1e2868c841f1","contact":"5df8ab5c355b1e2999c841f1"}]},{"_id":"6f4d01eb3b948150c2aad9c0","name":"Corp 1","externalId":"ie7iwkdsc"},{"_id":"5dg7aa8c366b1e2868c841f6","name":"Corp 2","externalId":"ahsdb34b"},{"_id":"5dg7aa8c366b1e2868c84111","name":"Corp 3","externalId":"ahsdb34b"}],"users":[{"_id":"5df8ab5c355b1e2999c841f7","firstname":"Caroline","lastname":"Glados","externalId":"d7f386c9-c69b-49c4-905c-90750c53dc22",},{"_id":"5df8ab5c355b1e2999c841f1","firstname":"jeff","lastname":"B","externalId":"11f386c9-c69b-49c4-905c-90750c53dc22",},{"_id":"5dg7aa8c366b1e2868c84111","firstname":"jhon","lastname":"B","externalId":"21f386c9-c69b-49c4-905c-90750c53dc22",}]}

Query

db.companies.aggregate([{$match:{_id:"5dg8aa8c435b1e2868c841f6"}},{$unwind:"$professionals_customers"},{$lookup:{from:"companies",localField:"professionals_customers.company",foreignField:"_id",as:"professionals_customers.company"}},{$lookup:{from:"users",localField:"professionals_customers.contact",foreignField:"_id",as:"professionals_customers.contact"}},{$addFields:{"professionals_customers.company":{$arrayElemAt:["$professionals_customers.company",0]},"professionals_customers.contact":{$arrayElemAt:["$professionals_customers.contact",0]}}},{$group:{_id:"$_id",professionals_customers:{$push:"$professionals_customers"},data:{$first:"$$ROOT"}}},{$addFields:{"data.professionals_customers":"$professionals_customers"}},{$replaceRoot:{newRoot:"$data"}}])

Result