Coaching
After a two-year hiatus from baseball, he became manager of the Padres' Northwest League affiliate Spokane Indians in 1993. The following season, he led the California League's Rancho Cucamonga Quakes to a 77–59 record, and in 1995, he was handed the reins to the triple A Las Vegas Stars. In 1996, he became third base coach for the Padres. He remained with manager Bruce Bochy's coaching staff through 2002. When Bochy was named manager of the San Francisco Giants for the 2007 season, Flannery joined him, and currently coaches third base for the Giants.
On Sunday, September 27, 2008, Flannery changed his number to 60 for one game because J. T. Snow came back from retirement and wore number 6. Snow was taken out before the first pitch.
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