In 2004–05, with 14 goals in 35 appearances, Flachi nearly helped Sampdoria earn UEFA Champions League qualification, with the team finally ranking fifth, with the subsequent return to the UEFA Cup. In the following campaign, he continued to display solid performances (again scoring in double digits), this time accompanied by Emiliano Bonazzoli up front; however, the team failed to qualify from the UEFA Cup group stage, and finished 14th in the league (12th after the match-fixing scandal).