Cruz was drafted in the third round (41st overall) of the 2009 MLS SuperDraft by the Houston Dynamo. He made his professional debut on March 28, 2009, coming on as a substitute in Houston's game against the San Jose Earthquakes. He scored his first goal for the Dynamo against DC United, he also had an assist in that game. In the 2011 season, Cruz was a big part of the Houston Dynamo team and scored a stunning goal at the end of the season against the Portland Timbers to help Houston get into the playoffs. He started in all four playoff games, including Houston's 1–0 loss to Los Angeles Galaxy in MLS Cup 2011.