Bieber will receive a $679,700 salary while in the major leagues and $311,600 in the unlikely event he is optioned to the minors.
Bieber was an All-Star in 2019 and led the major leagues during last year's shortened season in wins (eight), ERA (1.63) and strikeouts (122).
AdMets outfielder Jeff McNeil was renewed at a salary of $642,251 in the majors and $308,838 in the minors.
Another top young Mets player, left-hander David Peterson, agreed to a one-year contract with a salary of $585,750 in the major leagues.
Seattle outfielder Kyle Lewis, the reigning AL Rookie of the Year, was renewed for $625,000 in the majors and $282,750 in the minors.