Over the years, Cruz Azul's reserves have been a cornerstone for developing young talent and ensuring continuity between youth and senior football.

The current active reserve team is Cruz Azul Lagunas, which competes in the Liga TDP (Group II), the fourth tier of the Mexican football league system.

Cruz Azul Academy is the youth training system of the club, nurturing players from the U11 level to the U23 squad.

Joaquín Moreno serves as the Academy Director, overseeing all age groups and ensuring alignment with the club's philosophy.

[2] Since its formation, the academy has achieved notable success, including winning the U15 league championship during the Apertura 2018 tournament.

Several players have graduated from the academy to become prominent figures in Mexican football, including Fernando Bustos, Ignacio Flores, Octavio Muciño, Luis Hernández, Óscar Pérez, Francisco Palencia, Ricardo Osorio, Santiago Giménez, and Rodrigo Huescas, among others.

On 15 May 2014, the club's board finalized the sale of Cruz Azul Hidalgo, which became the new Zacatepec team for the Apertura 2014 tournament.

This restructured team continued to exist and competed in the Liga Premier de Ascenso of the Segunda División, preserving the legacy of the original club until it was disbanded in 2021.

Cruz Azul Jasso achieved significant success, becoming champions of the Segunda División in the Clausura 2007 tournament.

By the Apertura 2014 tournament, the club reverted to the Cruz Azul Hidalgo name following the sale of the Ascenso MX franchise to Zacatepec.

Its history dates back to 1986 when Cooperativa La Cruz Azul acquired a 46,600-square-meter piece of land with the goal of constructing its own facilities to replace the Seminario Menor de Acoxpa, where the team had been training while renting the property.

After transitioning to La Noria, Cruz Azul continued to use the Seminario Menor de Acoxpa for various activities, including youth team tryouts and training sessions.