Manager Mickey Callaway said Flores has early-onset arthritis in both knees and will receive injections to alleviate the pain.
"It's not like surgery is recommended at this time," Callaway said. "I think rest and a couple injections is supposed to knock this out pretty good."
Flores hit .267 with 11 home runs and 51 RBIs. He's started 73 games this season at first base, nine at third base and six at second base.