Villanueva spent most of his early life in different prisons for his political activities. In 1940, along with other APRA political activists, Villanueva was exiled to Chile. Between the 1940s and 1960s Villanueva spent his time in between Peruvian prisons and deportations to Chile and Argentina. While living in Santiago he met and married Lucia Ortega. They had a daughter: Lucia del Pilar Villanueva Ortega. 