Villegas' first taste of Major League Soccer action came in 1996, when he played three games for the MetroStars on loan from the New Jersey Stallions of the USISL.
Villegas' erratic play matched his versatility – brilliant one moment, awful the next – earning him the sarcastic nickname The Greatest Metro Ever.
Despite his inconsistency, he scored a number of key goals, including an overtime game winner in a comeback against the Tampa Bay Mutiny in 2000.
On May 10, 2002, the MetroStars traded Villegas and defender Orlando Perez to D.C. United for Craig Ziadie and Mark Lisi.
Villegas left MLS afterwards, going back to his native Ecuador to play for Aucas, Barcelona SC, Manta and Deportivo Cuenca.