Quad Cities, which plays in Modern Woodmen Park in Davenport, Iowa, replaces Lexington's affiliation with the Astros.
Astros general manager Jeff Luhnow worked with Quad Cities while serving as the St. Louis Cardinals' vice president of player development and scouting.
"I look forward to working with [owners] Dave Heller, Bob Herrfeldt, [general manager] Stefanie Brown and the rest of the River Bandits staff again," Luhnow said. "My experiences while with St Louis were very positive, and I know our players will benefit from their time in the Quad Cities."
Three current Astros players -- infielder Tyler Greene, first baseman Brett Wallace and right-handed pitcher Chuckie Fick -- played for Quad Cities while in the Cardinals system.
"We are genuinely excited to welcome the Astros family into one of the finest ballparks in the Minor Leagues and the community with the greatest fans in Minor League Baseball," Heller said.
In 1950, Astros Hall of Fame broadcaster and Iowa native Milo Hamilton landed his first job in professional baseball, broadcasting games for the Quad Cities Tigers in the very same ballpark that the River Bandits play in today.
The Quad Cities franchise joined the Midwest League in 1960. In addition to the Astros, the Major league affiliates include the Milwaukee (now Atlanta) Braves (1960-61), Los Angeles and California Angels (1962-78, 1985-92), Chicago Cubs (1979-84), Minnesota Twins (1999-2004) and St. Louis Cardinals (2005-12).
"We welcome the Astros back to the River Bandits family to continue building our shared history," Brown said. "Our fans will see the bright future of the Astros organization and some of the best young players in all of Minor League Baseball."