In the 2007–08 season, he captained the team to glory in the IPL after a six-year drought. During the 2008–09 season he was injured and missed many matches. He also missed matches because of the differences he had with the coach Nelo Vingada at the end of the season. He was the top scorer of the team for 2009–10 season and the most influential player on the team. In the second Sorkhabi derby of the season, Bagheri scored in the 87th minute with a trademark long-range shot to gain victory for Persepolis after six consecutive draws in the derby.