On December 3, 2011, following the acquisition of Chris Iannetta, he was traded to the Toronto Blue Jays for pitcher Brad Mills.

Nine days later, Mathis signed a contract with the Blue Jays to avoid arbitration.
He signed a one-year deal and was guaranteed to earn $1.5 million.
Mathis made his first career pitching appearance in a game against the Texas Rangers on May 25.
Pitching in the 8th inning, Mathis gave up a hit and walked a batter, but ended the inning without surrendering a run.
He became the sixth position player for the Blue Jays to pitch in a game, and the first since Mike McCoy on June 11, 2011.
 He made a second pitching appearance exactly two months later, mopping up in a 16-0 loss against Oakland.
 In that game, Mathis gave up 3 hits and 2 runs (both earned) in 1 inning of work.

On August 14, 2012, Mathis was signed to a two-year contract extension worth $3 million.
It included a 2015 club option worth $1.5 million.
Mathis was hitting .215 with six home runs over 147 plate appearances at the time of extension.
On December 3, 2011, following the acquisition of Chris Iannetta, he was traded to the Toronto Blue Jays for pitcher Brad Mills.
Nine days later, Mathis signed a contract with the Blue Jays to avoid arbitration. He signed a one-year deal and was guaranteed to earn $1.5 million. Mathis made his first career pitching appearance in a game against the Texas Rangers on May 25. Pitching in the 8th inning, Mathis gave up a hit and walked a batter, but ended the inning without surrendering a run. He became the sixth position player for the Blue Jays to pitch in a game, and the first since Mike McCoy on June 11, 2011.  He made a second pitching appearance exactly two months later, mopping up in a 16-0 loss against Oakland.  In that game, Mathis gave up 3 hits and 2 runs (both earned) in 1 inning of work.
On August 14, 2012, Mathis was signed to a two-year contract extension worth $3 million. It included a 2015 club option worth $1.5 million. Mathis was hitting .215 with six home runs over 147 plate appearances at the time of extension.
Jeff Mathis