His father Felipe, who managed Moises with the Expos from 1992 to 1996 and the Giants from 2005 to 2006, as well as uncles Matty and Jesús, and cousin Mel Rojas, all had long careers in Major League Baseball. In 2008, he was one of four active major leaguers (along with Prince Fielder, Ken Griffey, Jr., and Daryle Ward) to hit 20 home runs in a season whose fathers had also hit 20 home runs in an MLB season. He is the youngest of three sons born to Felipe and his first wife Maria Beltre, who raised him in the Dominican Republic after his parents divorced when he was two. His half-brother, Luis Rojas, is the manager of the New York Mets. Alou is married to Austria Alou; they have three sons: Percio, Kirby, and Moisés Jr.