2006–2011

Prior to the 2006 season, the Blue Jays signed Bengie Molina as the everyday catcher, making Zaun the backup.^[7] Zaun started 2006 on the injured list, with Jason Phillips serving as Molina's backup during the first week of the year. Zaun hit a game-winning two-run homer off the Tampa Bay Devil Rays' Jason Childers in his return on April 8.^[8] Molina's struggles against right-handed pitchers caused John Gibbons to platoon the two, with Molina generally starting against left-handed pitchers and Zaun playing against righties. On September 13, 2006, he hit home runs from both sides of the plate in the same game.^[9] He was only the fourth Blue Jay in history to do this.

Because the Blue Jays actively pursued Rod Barajas of the Texas Rangers as the club's new starting catcher during the 2006 offseason, it was assumed that Zaun would be exploring free agency as signing Barajas would mean Zaun would be maintained as a backup. Meanwhile, negotiations between Zaun and the club deteriorated, as Zaun claimed that the Jays offered "slightly better than back-up money for playing every day".^[10] Negotiations with Barajas went as far as an offer conditional on a routine physical, but eventually fell apart for undisclosed reasons.^[11] After turning down a reported $6.5 million two-year offer from the Blue Jays a week earlier,^[12] Zaun officially accepted a two-year, $7.25 million contract offer to return to the Blue Jays as their starting catcher on November 28, 2006. The new contract deal also included a third-year option, guaranteed based on appearances.^[13] The signing came after Zaun was rumored to have been courted by the Boston Red Sox and New York Yankees, both in backup roles.^[11]

Arguably his most famous play with the Jays was hitting a game-winning grand slam in the bottom of the 13th inning off of Tampa Bay Rays closer Troy Percival, on September 6, 2008, with two outs in the inning, wiping out the Rays, 7–4.^[14] Zaun hit only the second game-winning grand slam in Jays history but it was the first that occurred in extra innings, and even more spectacular was that his team was losing at the time, due to an RBI single by Dioner Navarro to put the Rays up, 4–3, before the slam at the top of the 13th.

On January 22, 2009, Zaun signed a one-year deal with the Baltimore Orioles.^[15]

Zaun was claimed off waivers by the Tampa Bay Rays GM Andrew Friedman in exchange for Rhyne Hughes on August 7, 2009.^[16][17] On August 16, Zaun hit a pinch hit grand slam home run against his old team, the Blue Jays, in the eighth inning off Brandon League on a 3–2 fastball.^[18] On November 12, 2009, Zaun was granted free agency.

On December 4, 2009, Zaun signed a one-year contract with the Milwaukee Brewers for $1.9 million.^[19] After suffering a severe injury, Zaun's 2010 season—and, as it turned out, his MLB career, ended on May 20.^[20] After the season, Milwaukee declined his contract option, and he became a free agent on November 2.^[21]

In January, Zaun signed a minor league deal with the San Diego Padres, with an invitation to spring training.^[22] However, noting that he still had not recovered from his previous injury enough to play regularly, he chose to retire on March 7, 2011.^[23]

Firing

On November 30, 2017, Rogers Communications announced Zaun's employment had been terminated after an investigation into complaints of improper conduct from several female employees.^[29] Zaun issued an apology in response to the allegations on December 4.^[30]

Glacier Range Riders

On March 30, 2023, Zaun was hired to serve as the catching/hitting instructor for the Glacier Range Riders of the Pioneer League.^[31]

Lexington Legends

On February 21, 2024, Zaun was announced as the manager for the Lexington Legends of the Atlantic League of Professional Baseball.^[32]