After the Revolution, Nakpil fell in love with and eventually married Bonifacio's widow Gregoria de Jesús. They moved to Manila and raised six children. Their eldest child and the only boy was Juan Nakpil who became a prominent Filipino architect and was recognized as a National Artist for Architecture. Another child married the architect Carlos Santos-Viola. Julio continued to compose until his death in 1960. Before his death he also contributed to a book on his life that was published by his heirs in 1964.