In 2001 López was named the Everett AquaSox Most Valuable Player by the Mariners player development department. Later that season he participated in the Arizona Fall League. He was also named the Mariners' minor league "Player of the Year."

He was named Mariners' minor league "Player of the Year" with the San Bernardino Stampede in 2002, marking the second time he won this award. He led the California League with 169 hits and 39 doubles. His .324 average was second-highest among all Marines minor leaguers while his 31 steals ranked fourth. Later that year selected to play with the World Team at the 2002 MLB Future's Game in Milwaukee.

López played three different infield positions (second base, shortstop and third base) in 132 games with the Double-A San Antonio Missions in 2003. He was third in the Texas League with 35 doubles. He had 41 multi-hit games, including four 4-hit games. At the all-star break he was selected to start for the Texas League. At the end of the season he was named to Texas League Postseason All-Star Team. López hit .391 with 3 runs, 2 home runs, a steal and 5 RBIs in five postseason games. He again played with Lara in the Venezuelan Winter League.

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