Thanks to the mediation of Dr. Hermán Bueno Ramírez, the three co-founders reached a compromise to merge the previous clubs into a new entity named Once Caldas.

The merged club joined the league ahead of the 1961 season under the license that formerly belonged to Deportes Caldas,[7] and played its first match on 12 March 1961, a 3–2 loss to Deportivo Pereira.

The season was divided into two tournaments, Copa de La Paz (Apertura) and Torneo Nacional (Finalización).

[7] The Copa CONMEBOL was Once Caldas's first participation in an international competition, in which the club was eliminated in the first round by the eventual winners Santos.

They topped the Torneo Apertura with 77 points as well as the Finalización, and went on to win their semifinal group to set up a final with Deportivo Cali, in which Caldas were heavy favorites.

Once Caldas participated in the Copa Libertadores for the first time in 1999, with their group consisting of Deportivo Cali, Vélez Sársfield and River Plate.

After an outstanding campaign in the knockout rounds in which Once Caldas successively eliminated Ecuadorian side Barcelona as well as the previous season's finalists Santos and two time champions São Paulo, Once Caldas reached the finals where they were paired up with five-time champions Boca Juniors.

In the second leg in Manizales, Once Caldas took the lead with a goal by Jhon Viáfara but Nicolás Burdisso leveled the score in the second half to send the match into a penalty shootout which was won by the club 2–0, and Once Caldas, managed by Luis Fernando Montoya, won the competition for the first time ever, becoming the second Colombian team after Atlético Nacional to win the Copa Libertadores.

In 2005, as the previous year's champion, Once Caldas tried to defend its title in the Copa Libertadores, but were eliminated by Tigres UANL in the round of 16.

[10] Following the Kenworth takeover, the team qualified for the final stages of both the Apertura and Finalización championships during the 2013 and 2014 seasons.

The following year they took part in the Copa Sudamericana for the first time, losing to Paraguayan side Deportivo Santaní in the first round.

[13] After concluding its contract with Adidas, Once Caldas switches to Peruvian company Walon Sport, since the 2008 season.

Once Caldas plays its home matches at Estadio Palogrande, located in Manizales and inaugurated in 1936 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.