Following his first retirement, Vázquez followed a practice done also by other pugilists, such as Juan Laporte, Félix Trinidad, Julio César Chávez, Bobby Czyz, Sean O'Grady, Sugar Ray Leonard, Santos Laciar, Lennox Lewis, Roy Jones Jr. and Héctor Camacho among others, deciding to become a boxing commentator. Since he was sure that this retirement was definitive, the pugilist joined Univision and began narrating fights along the network's other sportscasters. Following his second retirement, Vázquez began working as a boxing trainer. Under this office, he has most notably trained his two sons, Wilfredo and Israel. Vázquez, Jr. debuted as a professional on December 8, 2006, being managed by Rubén Zavala and his promotion All Star Boxing. Vázquez has expressed that he didn't want his son to become a boxer, expecting him to study and develop a profession within the fields of law, but he accepted to train him after noticing real interest, despite knowing that he lacked any amateur experience. Subsequently, he noted his interest to be one half of the first father and son duo to win world championships in Puerto Rico. On September 12, 2008, Vázquez, Jr. won his first professional championship, the WBO Latino super bantamweight title, before incorporating the WBA Fedecentro super bantamweight title to his résumé two months later. On February 27, 2010, Vázquez, Jr. won the WBO's super bantamweight world championship joining his father as the third father-and-son combination to win world championships. They also became the first to do so in the same division. Israel Vázquez debuted on his brother's second defense, competing in the light flyweight division.

Outside of the championships won as an active boxer, Vázquez also received other recognitions due to his work. In 1996, he received the Frank Parilla Award from the Puerto Rico Boxing Commission, which is awarded to the boxer that is universally regarded as the best Puerto Rican Boxer of the year. He won this recognition after he made history by becoming the first boxer to win three separate titles within the same organisation, in this case the World Boxing Association. That same year, the WBA gave him the award for "Best Latin American Boxer of the Year". Vázquez subsequently commented that he expected to win the "Boxer of the Year" award that was won by Evander Holyfield, but he accepted the selection under the circumstances. He is the only Puerto Rican boxer to be honored by having a long-distance foot race named after him, with the "Maratón Wilfredo Vázquez" being held annually in Bayamón since 1988.

Prior to many of his fights, Vázquez spent months training for them at Toluca, Mexico, a city that was also favored by such other boxing luminaries as Chávez and Salvador Sánchez for such practice