He became a coach for the Savannah Sand Gnats in 2010 but transferred back to manage the Gulf Coast League Mets in 2011.

On his return to Savannah from 2012 through 2014, Rojas won the 2013 South Atlantic League championship and was named Manager of the Year the following season.

[4][5] Rojas managed in the Dominican Professional Baseball League team Leones del Escogido.

[9] Rojas was promoted to manager by Mets general manager Brodie Van Wagenen on January 22, 2020, after the Mets mutually parted ways with Carlos Beltrán due to his involvement in the Houston Astros sign stealing scandal.

[11] Van Wagenen lost his job at the end of the pandemic-shortened season and was replaced by Sandy Alderson, who had a long relationship with Rojas and kept him on.

[12] On April 20, 2021, Rojas was ejected from a game for the first time in his Major League career after arguing balls and strikes with home plate umpire John Libka.

[15][16] The Mets were the first team in major league history to sit atop a division for more than 100 days in a season and finish with a losing record.

Rojas' mother is Elsa Brens, Alou's third wife, a secretary for owners of the Dominican summer league.