How to update value inside an array from multiple array in Mongoose?
You could use the $ positional operator in the findOneAndUpdate method.
Model.findOneAndUpdate({"username": req.body.Email, "organization.idOrganization":"54c8b01af927db992d021f58"}, {$set:{"organization.$.displayname":req.body.Displayname}}, {}, function(err,resp){//handle response})