His salary will increase $100,000 if he wins a third Gold Glove award this fall. Next season is the final year of Gonzalez's team-friendly $9.5 million, four-year contract.
Also on Monday, right-hander Jon Garland declined his mutual option and became a free agent.
Gonzalez, who grew up in the San Diego area and was the No. 1 overall pick by Florida in the 2000 amateur draft, might be too expensive for the Padres to keep.
He was obtained in a trade with Texas before the 2006 season and has blossomed into one of the game's best first basemen. He hit .298 with 31 homers and 101 RBIs last season for San Diego, which fell just shy of a playoff spot.