Retired to stand at stud at Castleton Farm, Commando proved to be a successful sire. Unfortunately he died on March 13, 1905 at age seven after developing tetanus from a cut sustained to his foot. He was buried at Castleton Farm. Although his breeding career was limited to four seasons, Commando produced 10 stakes winners from 27 foals and posthumously topped the U.S. sire list in 1907. Among his progeny were Hall of Fame champions Colin and Peter Pan.
Following its creation, in 1956 Commando was inducted posthumously into the National Museum of Racing and Hall of Fame. A painting of Commando by equine artist Charles L. Zellinsky is on display as part of the Museum's collection.