In 1999, the Chicago Bears moved Parrish from free safety to strong safety where he started all 16 games. He improved during his second year in the NFL, recording a career-high 124 tackles, which was second on the team. In week 11 of the 2000 NFL season, Parrish returned an interception for a touchdown against the Tampa Bay Buccaneers in the second quarter, which eventually secured a win for the Bears with a final score of 13-10. In 2000 and 2001, he had three interceptions each year, starting every game each year at strong safety. In 2001, Tony’s last year with the Bears, he paired with Mike Brown (free safety) to be one of the leading safety duos in the NFL. In 2001, he helped lead the bears' defense in giving up the fewest points in the NFL. The Bears finished as Champions of the NFC Central with a 13-3 regular season record.