In the Padres organization as a starter, Clay started 43 games between the Triple-A Portland Beavers and the major leagues, giving up 118 earned runs in 257.1 innings (ERA of 4.13).

After being converted to relief, he was off to a strong start in 2006 as well, allowing only 3 earned runs in eight appearances, but was called up to the Phillies in May.

Condrey would be designated for assignment three other times, up until August 3, 2007, when he was recalled from Triple-A Ottawa for his fifth stint of the season with the Phillies.

Condrey was included on the postseason roster for the National League East Champion Phillies in 2007 and appeared in Game 2 of the NLDS against the Colorado Rockies.

Condrey went 6–2 with one save and a 3.00 ERA in 45 appearances for the Phillies in 2009, but was not included on the postseason roster as Philadelphia returned to the World Series before falling to the Yankees in six games.