His first managerial job in professional soccer came when he was hired as assistant coach to Thomas Rongen – later replaced by Ray Hudson – at D.C. United, a position he occupied from 2001 through 2002. In the latter year, Onalfo left to become an assistant to Bruce Arena during the 2002–2006 stretch of Arena's tenure as coach of the U.S. national team. In 2005, Onalfo was included among the final three candidates for the top job at the Colorado Rapids, eventually being passed over for Fernando Clavijo.