In the Apertura 2009, the club began the tournament by signing players Jared Borgetti, Nicolás Martínez, Nicolás Vigneri, Carlos "El Pescadito" Ruíz and the return of Joaquín Velázquez and Nicolás Olivera, who had been on loan to Tiburones Rojos de Veracruz. The club quickly adapted with the new players and did not see a loss until the 10th round. It was a controversial game were Puebla lost against Monterrey due to bad calls and a disallowed goal that was proven to be legit. The club once again finished with 26 points, by means of 6 wins 9 draws and 4 losses, which qualified them to the quarter-finals. Cruz Azul was the opponent in that series, and the first match was held in Puebla, where the game ended in a 4–4 draw with Puebla scoring 4 goals in the first half. Cruz Azul scored 2 polemic goals which determined to be crucial in the outcome of the series. The second match was held in the Estadio Azul; the game ended in a 3–2 victory for Cruz Azul, where once again controversy occurred, when Cruz Azul scored its first goal that was a clear offside. Cruz Azul advanced and eventually made it to the final, which they lost to Monterrey. And so it came to an end, with Puebla having qualified to 2 consecutive playoffs, not since the 1991–1992 tournament.