All players have a low conditioning at the start of the season, it's higher if they attend training camp but they do need actual game time to get fully into game shape. So it's up to you to try to balance giving him enough playing time without risking injury.
I have found that pulling starters after:
game 1: 1st quarter
game 2: 2nd quarter
game 3: 3rd quarter
game 4: 1st quarter
seems to have the best balance of getting your players conditioned without risking too much injury to your starters.