Lobaton hit .259 with 76 hits in 294 at-bats with the San Antonio Missions. He collected 21 doubles, nine homers, 35 runs scored, and 45 RBIs across 92 games. He also drew 39 walks compared to 75 strikeouts for a .338 on-base percentage and stole one base in two attempts. Lobaton threw out 30-of-112 base runners attempting to steal, good for 26.8 percent.

2007

Lobaton hit .260 with 79 hits in 304 at bats for the Lake Elsinore Storm. In 90 games he had 15 doubles, three triples, 10 homers, 50 runs scored and 47 RBIs. He drew 41 walks compared to 79 strikeouts. Lobaton threw out 42-of-142 basestealers, 29.6 percent.

Lobaton hit .273 with two doubles, five RBIs and seven runs scored over 12 Storm playoff games.

2006

Lobaton joined the Fort Wayne Wizards after hitting .213 with seven doubles, four home runs, 15 RBI and 12 runs scored in 42 games for the Lake Elsinore Storm.

Lobaton hit .279 with 17 hits in 61 at bats for the Wizards. In 20 games he collected three doubles, one triple, a homer, 11 RBI's and 15 runs scored. He also walked 12 times while whiffing the same amount. He ended the year with an 8-game hitting streak.

2005

Lobaton hit .281, going 9-for-32, in 11 games for the Ems in 2005.

Lobaton hit .357 in five games with the AZL Padres, walking six times compared to four strikeouts.

Lobaton went 6-for-34 in nine games for Fort Wayne in 2005.