He has played in Major League Baseball (MLB) for the San Diego Padres, Tampa Bay Rays, Washington Nationals, New York Mets, and Chicago Cubs.

Lobatón made his professional debut in 2003 with the rookie ball Idaho Falls Padres, slashing .272/.352/.366 in 56 games.

In 2005, he split the season between Eugene, the AZL Padres, and the Single-A Fort Wayne Wizards, accumulating a .250/.368/.313 slash line with 6 RBI between the three teams.

In 2006, he split the year between the High-A Lake Elsinore Storm and Fort Wayne, posting a .235/.355/.383 batting line with 5 home runs and 26 RBI.

In 2008, Lobatón played for the Double-A San Antonio Missions, logging a .259/.338/.422 slash line with 9 home runs and 45 RBI.

On July 30, 2009, Lobatón was claimed off waivers by the Tampa Bay Rays and was assigned to the Double A Montgomery Biscuits, where he finished the year batting .262 in 26 games.

In 2010, Lobatón spent the entire season split between Montgomery and the Triple-A Durham Bulls, posting a .260/.339/.385 slash line with 7 home runs and 35 RBI.

[7] On February 13, 2014, Lobatón was traded to the Washington Nationals (along with Felipe Rivero and Drew Vettleson) in exchange for Nathan Karns.

He finished the year with the Triple–A Oklahoma City Dodgers, posting a batting line of .234/.339/.383 with one home run and five RBI in 15 games.

[21] On February 12, 2021, Lobatón re-signed with the Cubs on a minor league contract that included an invitation to Spring Training.

[23] In a June 29 game against the Milwaukee Brewers, Lobatón sprained his shoulder attempting to avoid a collision with Josh Hader at first base.