It was during this spell did the club hit their golden period as they had several renowned players including Jesus Gonzales, Carlos “Carlanga” Rivera, Joaquín Valencia, Ricardo “la Tuca” Gómez, Jesús González Barillas, Efrain Yin Gonzalez Óscar "Lotario" Guerrero, Jose Maria Rivas, Ramón Maradiaga and Jorge González.

In 2006, the owners of Coca/Cola later renamed Nacional 1906 approached Independiente FC, the board voted on merging the club forming Independiente Nacional 1906, this was the shot in the arm the club needed as they won promotion to Primera division, however the poor results led the team to the decline in the 2007 Clausura.

getting half a ticket to the Major League, would return to final instances in the 2017 Clausura, but would fall with Audaz both in the final series of the tournament, and in the first defining party[1] In 2019, for the start of the Tournament 2019 Clausura it is announced that the club's leadership acquires the team's franchise Audaz,[2] which due to economic problems and debts can not continue to hold in the first division, although for reasons of logistics handling in the tournament with the name and distinctive of the apastepecano club[3] At the end of the 2020 season, Pablo Herrera (owner of the franchise license) announced that Independiente will lose their license and he will be giving the license to Luis Angel Firpo for the Clausura 2020.

[4] After four year hiatus, Independiente FC announced on June 15, 2024 they had purchased Estrella Roja and will complete in the 2024-2025 Tercera Division season.

They gave a spectacular tribute in the 19th minute to Erasmo Henriquez, a player who died a year earlier from an illness, this bar has also lost three of its members 'Manyula' was the leader, 'Chato' and the 'Pijuyo' were always present.

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

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