He worked his way up to Triple-A in 2005, where he was an All-Star outfielder and the San Diego Padres Minor League Player of the Year, hitting .312 with 25 home runs.

He was not selected for San Diego's 2006 playoff roster, and after the season ended he was traded to the New York Mets with relief pitcher Jon Adkins in exchange for relievers Heath Bell and Royce Ring.

During June, he received some playing time when all three Mets regular outfielders (Shawn Green, Carlos Beltrán, and Moisés Alou) were injured.

However, the Mets brought Johnson back by signing him to a minor league deal on February 14, 2008, and invited him to spring training.

In 2009, Johnson attempted a comeback from multiple injuries with the Orange County Flyers of the Golden Baseball League.