Four days after being released by Reading, Convey returned to MLS, signing with the San Jose Earthquakes. He scored his first goal for the Quakes on April 11, 2009, against the Chicago Fire, while playing left-back. In 2010, Convey recorded 10 assists and was given the MLS Comeback Player of the Year Award. After a fractious relationship with manager Frank Yallop, it was announced that Convey would not be returning to San Jose for the 2012 season. In his three seasons at the club, Convey appeared in 75 league matches and scored three goals.