Puebla obtained only 20 points in the Winter 1999 tournament, and José Mari Bakero was replaced by Mario Carrillo as coach. In the summer of 2000, Miguel Mejia Barón took over as head coach, and the club qualified for quarter-finals, after beating Atlas 5–1, where they lost 9–0 on aggregate to Toluca. They again reached the quarter-finals the following season, where they beat Tigres UANL 5–3. In the semi-finals against Santos Laguna, Puebla won a dramatic first leg 5–4. The second leg finished 2–1 to Santos, with Puebla being knocked out due to their inferior league-standing.