Italy midfielder Matteo Pessina scored a second-half winner as Atalanta edged out Young Boys 1-0 on Wednesday to move top of their Champions League group.
The Serie A side, bidding to reach the knockout stage for a third straight season, have four points from two Group F games after an opening 2-2 draw at Villarreal.
Manchester United, who lost to Young Boys a fortnight ago, host Villarreal later on Wednesday in a repeat of last season's Europa League final, won by the Spaniards on penalties.
Gian Piero Gasperini's Atalanta have now lost only one of their last 11 Champions League group matches and they next face two games against United.
"There was great enthusiasm from the fans," Gasperini told Sky Sport. "The Champions League is tough, the teams are quick.
"Now we face Manchester United, two crucial matches for qualification."
Atalanta thought they had taken an early lead when Sandro Lauper put through his own net, but Rafael Toloi was adjudged offside after a VAR review.
The hosts dominated possession only to struggle in front of goal, with Young Boys goalkeeper David von Ballmoos saving from Toloi and Davide Zappacosta.
Pessina made the breakthrough though with his first Champions League goal in the 68th minute, diverting the ball into the roof of the net from close range after Duvan Zapata did brilliantly to keep it in play.
Young Boys were never able to exert the same pressure they put on the 10 men of Manchester United, with Luis Muriel, back from injury as a substitute, and Zapata both missing chances to score a second for Atalanta.