Although the team had played Mexican professional football for 70 years, it had never won a first division tournament until winter 2000, when the club raised the cup after beating Toluca on penalties.

On November 5, 2013 Monarcas Morelia won their first Copa MX title in a 3–3 match that went to penalties, where they would take the victory.

This title also allowed them to participate in the inaugural edition Supercopa MX, which they won against Tigres UANL with a global score of 5–4.

After no notable improvement in team performance, Meza was let go from the position of head coach in 2016, with Roberto Hernandez taking over as interim manager.

Hernandez's tenure would coincide with the signing of Peruvian forward Raul Ruidiaz on loan from Universitario.

[6][7][8] The club's owner, Grupo Salinas, reportedly were asking for $400 million MXN per year from the Government of Michoacán to keep the team in the city.

[10] Despite stay-at-home orders due to the COVID-19 pandemic, over 7,000 fans took to the streets of Morelia to protest the team's move.

[12] On June 26, 2020, Liga MX President Enrique Bonilla announced Atlético Zacatepec would be relocating to Morelia due to financial problems.

[14] It was announced the ownership group would consist of former Guadalajara President José Luis Higuera as well as various businessmen from the state of Michoacán.

On April 9, 1989, after several construction delays, Stadium Jose Maria Morelos and Pavón (located on the outskirts of the Quinceo mountain) was opened, and the inaugural game was between Atlético Morelia and Club América.

Adolfo Bautista, Rafael Márquez Lugo, Moisés Muñoz, Miguel Sabah, Joel Huiqui, Adrián Aldrete, Enrique Pérez, Édgar Lugo and Elias Hernandez, are some of the players that were called up to the Mexico national team while playing with the team.

Raul Ruidiaz was the first Morelia player to achieve a Liga MX top scoring title.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.