In 1968 he earned a bachelor's degree in business and financial administration from the University of Puerto Rico.
On October 18, 1976, Pesquera was sworn in as Special Agent of the Federal Bureau of Investigation (FBI).
Once he completed inicial training at the FBI Academy in Quantico, Virginia he was assigned to San Juan, Puerto Rico, where he worked in the organized crime, counterintelligence, and terrorism divisions.
In July 1982, Pesquera was transferred to Tampa, Florida, where he worked on terrorism and international counterintelligence matters.
He then served as Coordinator for the United States Department of Homeland Security at the Broward County Sheriff's Office from 2003 to 2008, and as Assistant Director of Safety Affairs of the Port of Miami from 2008 to 2012.