Early into the 1979 season, Stein was placed on the disabled list after suffering a rib injury. Charlie Beamon, Jr. was called up from the minor leagues to replace Stein during his injury. In late June, the Mariners activated Stein from the disabled list. By the time he had returned, the Mariners had already positioned Dan Meyer at his position, so Stein filled in at second base during his first game back. That year, Stein batted .248 with 28 runs scored, 62 hits, nine doubles, two triples, seven home runs, and 27 RBIs in 88 games played. As a fielder, he played 67 games at third base, 17 games at second base, and three games at shortstop.