The president of the National Amateur Football Commission, Luis Duarte Plata, had planned to replace Copa Perú with the Liga 3 and hold the last edition in 2020; during the Departmental Stage of said tournament, the 25 champions would participate in the first edition of Liga 3 in 2021.

[3] However, the Peruvian Football Federation decided to cancel the 2020 edition of the Copa Perú while the District Stage was in development due to the COVID-19 pandemic, which resulted in the pause of the creation of the Liga 3.

This idea was embodied by President Agustín Lozano through the "reforms of Peruvian football", which would have as their first important change the elimination of promotion to the First Division from the Copa Perú.

[5][6] In 2024, the Peruvian Football Federation, taking into account CONMEBOL's observations, then decides that the Copa Perú would be the tournament that decides the participants in a meritorious manner, based on the original idea from years ago: the 25 representatives of each department that are best placed in the final table of the 2024 Copa Perú's National Stage, whether the departmental champion or runner-up and except for those promoted to Liga 2, will be the clubs that will play the first edition of Liga 3 in the year 2025.

However, after the administrative relegation of Unión Huaral and Juan Aurich, from the 2024 Liga 2 at the beginning of the season, in addition to the increase to eight of the qualifiers since the 2024 Torneo de Promoción y Reserva, this number was expanded to 36.