On November 15, 2016, Cora became the bench coach for the Houston Astros. Cora assumed managerial duties on three occasions during the 2017 season, following ejections of Astros manager A.J. Hinch.
On August 25, 2017, Cora was ejected from a game against the Los Angeles Angels by home plate umpire Laz Díaz. Cora argued that the baseball had too much dirt on it and should be removed from play; this was Cora's first career MLB ejection.