After injuries ended his playing career, Minaya joined the Texas Rangers' scouting team in 1985, where he helped in the signing of players such as Sammy Sosa,[5] Juan González, and Ivan Rodriguez.

In the mid-1990s, Minaya left Texas and returned home to join the staff of the New York Mets, working his way to assistant general manager behind Steve Phillips and being partly responsible for that team's late-1990s success.

[6] This unusual ownership arrangement was reached after an attempt at contracting the Expos failed, while MLB set up a three way deal in which John W. Henry, the owner of the Florida Marlins, was allowed to purchase the Boston Red Sox, while the Expos' owner, Jeffrey Loria, was permitted to sell the Montreal club and purchase the Florida Marlins instead.

[7] With the fan base rapidly declining and speculation that the team would be relocated, Minaya was forced to work with limited financial resources.

On July 11, he acquired Cliff Floyd from the Marlins only to deal him to the Boston Red Sox for Sun-Woo Kim and a minor leaguer by the end of the month.

When it was announced the Expos would relocate to Washington, D.C. for the 2005 season, Minaya learned with the move would come a whole new front office and coaching positions.

In Minaya's first offseason he made two significant free agent signings, adding pitcher Pedro Martínez and outfielder Carlos Beltrán.

Minaya's work in the 2005 offseason would further shape the franchise, adding closer Billy Wagner, first baseman Carlos Delgado and veteran catcher Paul Lo Duca.

He also strengthened the bench by adding utility infielder José Valentín, first baseman Julio Franco and outfielder Endy Chávez.

Despite the veteran additions, Minaya was able to limit payroll by trading Mike Cameron to the San Diego Padres for Xavier Nady and Kris Benson to the Baltimore Orioles for Jorge Julio and John Maine.

Minaya also traded away several young pitchers many fans believed could have helped the Mets avert their historic breakdown at the end of the 2007 season.

A few days later, he sent hard-throwing relievers Henry Owens and Matt Lindstrom to the Florida Marlins for lefties Jason Vargas and Adam Bostick.

Minaya was subject to intense scrutiny and criticism from many in Major League Baseball and by the New York City media for his handling of the firing of Willie Randolph as the Mets manager.

Many members of the media and fans criticized the timing of the decision, a day into a west coast road trip, and some referred to the late night episode as the Mets' "Midnight Massacre."

[12] At the press conference announcing the firing, Minaya angrily challenged the accuracy of past news reports, claiming New York Daily News reporter Adam Rubin, who initially broke the story about Bernazard challenging Binghamton Mets players to a fight, was angling for a position in the Mets organization.

[16] Minaya left the position in January 2015 joining the Major League Baseball Players Association as a senior adviser to executive director Tony Clark.

As stated by mlb.com writer Anthony DiComo, "the council serves as a catalyst to promote health and fitness through participation in physical activity and sports."