The Houston Dynamo announced on April 14, 2009, that they had secured Hainault's international transfer certificate from Most; he had been training with the team throughout the 2009 pre-season.
Hainault was signed to a standard four-year MLS contract and made a base salary of $55,125 in 2009.
He made his MLS debut for Houston on May 3, 2009, coming on as a substitute for Wade Barrett in a game against New England Revolution.

Hainault turned down a call-up for two 2014 FIFA World Cup qualification matches due to an important club match-up against the Portland Timbers on October 15, 2011.
It turned out to be a major factor in the game, with Hainault scoring his first goal of the season and opening goal of the game from a Brad Davis free kick.
Houston went on to a 2–0 away win, clinching a playoff spot.
Later in 2011, he scored two playoff goals, including the opening goal in a 2–0 win in the Eastern Conference Final of the 2011 MLS Cup Playoffs, sending the Dynamo to their first MLS Cup since 2007.
Houston fell to the Los Angeles Galaxy on November 20, 2011, in a 1–0 final, with a goal from Landon Donovan.

After an off-season with much speculation of a transfer to Bordeaux, Hainault remained in Houston for 2012 and scored the game-winning goal over Chivas USA in the season opener on March 11, 2012.
The Houston Dynamo announced on April 14, 2009, that they had secured Hainault's international transfer certificate from Most; he had been training with the team throughout the 2009 pre-season. Hainault was signed to a standard four-year MLS contract and made a base salary of $55,125 in 2009. He made his MLS debut for Houston on May 3, 2009, coming on as a substitute for Wade Barrett in a game against New England Revolution.
Hainault turned down a call-up for two 2014 FIFA World Cup qualification matches due to an important club match-up against the Portland Timbers on October 15, 2011. It turned out to be a major factor in the game, with Hainault scoring his first goal of the season and opening goal of the game from a Brad Davis free kick. Houston went on to a 2–0 away win, clinching a playoff spot. Later in 2011, he scored two playoff goals, including the opening goal in a 2–0 win in the Eastern Conference Final of the 2011 MLS Cup Playoffs, sending the Dynamo to their first MLS Cup since 2007. Houston fell to the Los Angeles Galaxy on November 20, 2011, in a 1–0 final, with a goal from Landon Donovan.
After an off-season with much speculation of a transfer to Bordeaux, Hainault remained in Houston for 2012 and scored the game-winning goal over Chivas USA in the season opener on March 11, 2012.
André Hainault