Atletico Huila

The club was founded on 29 November 1990 and was admitted into the Categoría Primera B tournament the following year. In 1992, Alberto Rujana was appointed as manager. That same season, the club purchased midfielder Guillermo Berrío from América de Cali; Rujana named him captain and made him the centerpiece of the squad. As a result, promotion to the top flight followed. The club managed to last in the top flight until the end of the 1996–97 season, when they finished last in the relegation table and were sent back to Primera B.

Rafael Corrales took over the club in 1997, and led them to an immediate promotion back to the top flight. The club managed to consolidate itself in the league, although relegation was a constant danger. Huila escaped relegation only on goal differential in 2002 and had to win a relegation playoff against Valledupar in 2006. This was why the club's performance in 2007 was almost entirely unexpected.

Under the management of Néstor Otero for the 2007 season, the club finished third in the Apertura and qualified for the semifinal phase. They further surprised by winning their semifinal group (beating Millonarios on the final day of the round robin) to reach the Apertura finals, where they were beaten by Atlético Nacional 2–1 over two legs. A similarly unexpected result came in the second half of the 2009 season (Finalización tournament), when the club finished third in the first stage and topped its semifinal group. Once again they were beaten in the finals, this time by Independiente Medellín by a 3–2 aggregate score. The strong performance in the 2009 season allowed Atlético Huila to qualify for the following year's Copa Sudamericana for the first time in history, in which they beat Venezuelan team Trujillanos in the first stage, but were knocked out by San José from Bolivia in the second stage.

The club placed first in the first stage of the 2015 Torneo Apertura, however they were eliminated in the quarterfinals by Deportes Tolima.

After 22 years in the top flight, Atlético Huila were relegated back to the second tier at the end of the 2019 season, finishing in last place of both the relegation table and the year's aggregate table. Their relegation was confirmed on the last day of the regular season with a 1–0 defeat against Jaguares, who were also involved in the relegation struggle.

Following their return to Primera B, Atlético Huila won the 2020 tournament, which did not grant promotion for the following season given that promotion and relegation were postponed for six months due to the effects of the COVID-19 pandemic in Colombia, however they were able to seal their promotion back to Primera A by beating Deportes Quindío, winners of the first tournament of the 2021 season, in a double-legged grand final. Although their return to the top flight was short-lived and they were relegated back to Primera B at the end of 2021, in their return to the second tier for the 2022 season they were able to bounce back from a poor performance in the first half of the season by winning the Torneo II which allowed them to qualify for the Primera B Grand Final against the Torneo I winners Boyacá Chicó. Their defeat in that series forced them to play a double-legged play-off against Deportes Quindío for the final promotion spot, which they won by beating the cuyabro side by a 2–1 score on aggregate, allowing them to return to Primera A for 2023.

On 4 May 2023, 97.203% of the club's shares were sold to the international holding Sociedad FARLAY S.A. led by businessman Michel Deller, who also owns the Ecuadorian club Independiente del Valle. That same year, Atlético Huila suffered a fourth relegation to the second tier, after a poor performance in the first half of the season.

The failed refurbishment works of Estadio Guillermo Plazas Alcid, which were paused since 2016 following the death of two workers after a section of a grandstand collapsed, posed a problem for the club in its later years. After playing away from Neiva while the stadium was closed, in 2018 Atlético Huila had to invest on temporary locker rooms as well as the stadium's lighting system in order for it to be enabled to host games. Without a definitive solution from government entities for the reconstruction of the stadium, it was permanently closed due to its structural damage on 28 October 2025, forcing the club to look for a new stadium to host their games. On 14 November 2025, the club announced an agreement with the local authorities of Yumbo, Valle del Cauca Department to move there, pending approval from Dimayor. On 11 December 2025, the Assembly of Dimayor approved the move. As part of the agreement reached with the Yumbo Municipality, the club ceased to play as Atlético Huila, making way for a new club named Independiente Yumbo.

On 25 December 2025, Maruan Issa, club chairman since 2023, handed over the Atlético Huila brand to local businessman Felipe Olave, who sought to build a new stadium for the club as well as returning it to professional competition by acquiring another club's license.