Born in Utuado, Puerto Rico, Maldonado migrated to New York City when he was 12. In 1968, he enrolled at the San Francisco Art Institute where he continued his training as a photographer and as a master printer. In the early 1970s, Maldonado co-founded and co-directed the Foto-Gallery in Soho with Alex Coleman, which focused on photography and photo-derived works.

Among his best-known works are a series of iconic portraits of Puerto Rican cultural figures such as Tito Puente, Marc Anthony, Rita Moreno, Pedro Pietri and Clemente Soto Vélez. Together with Pietri, and over the course of more than a decade (1994-2012), Maldonado also co-produced an influential conceptual project on Puerto Rico's colonial status, "El Puerto Rican Embassy," which encompassed the creation of objects such as "El Puerto Rican Passport," an art passport issued by the artists that featured personal information and an out of focus photograph of the bearer. From 1994 through 2016, Maldonado likewise produced a series titled Coconauts in Space, where he retells the story of the first human landing on the moon. In his version the first to land were not Americans in 1969 but several Puerto Ricans who planted the Puerto Rican flag in 1963.

Maldonado also published various books featuring his photography and literary work, including The Evidence of Things Not Seen (1975), Out of Focus Nuyoricans, (2004), I Love my Selfie (2017) Mambo Madness: a Novel (2016), Cuerpo del poema (2017), and Puerto Ricans Underwater/Los ahogados (2017).

Maldonado's work has been acquired or exhibited by the National Portrait Gallery, the Metropolitan Museum of Art, Museum of Modern Art, Museo del Barrio, and the Museé Modern de la Ville de Paris France, among many others.