Nacional is the only Colombian club that has won the two domestic short-format tournaments in a single year, Apertura and Finalización, since the format was established in 2002, winning the titles of the 2007 and 2013 seasons.

Economic troubles plagued the team in the late 1950s, and during 1958 the club was briefly forced to merge with crosstown rivals Independiente Medellín.

The revival had actually started after the 1970 season, with the hiring of manager José Curti and the signing of midfielder Jorge Hugo Fernández.

They qualified for the final stage by winning the Torneo Finalización with 34 points, then finished first in a three-way round robin against Millonarios and Deportivo Cali.

With his strong emphasis on conditioning and physical play, Zubeldia was able to manage the club to two further titles, 1976 and 1981, as well as regular finishes towards the top of the table.

Nacional remained a power in Colombia, but the death of their manager, the departure of Cueto, and the rise of América de Cali (the Red Devils won five straight championships in the 1980s) left its fans dissatisfied, and began a decade-long trophy drought.

The two goals were complementary; Atlético Nacional's traditional preference for Colombians over foreigners made them a natural base for Maturana to build his national team upon.

The midfield featured Leonel Álvarez (capped over 100 times for Colombia) and Alexis García (team captain and Medellín native).

[15] The entire focus of the 1989 campaign was on the Copa Libertadores, which Atlético Nacional hoped to become the first Colombian club to win the competition.

In the group stage, Los Verdolagas were placed with fellow Colombian side Millonarios, as well as Ecuadorian clubs Deportivo Quito and Emelec.

Nacional answered in the second leg (played in Bogotá on the grounds that the Estadio Atanasio Girardot in Medellín was too small) with a 2–0 win of their own.

[21] Whilst the club hit that milestone abroad, the domestic league season was cancelled due to the assassination of referee Álvaro Ortega on 1 October after a match between Independiente Medellin and America de Cali.

[28] Juan Daniel Cardellino, an Uruguayan referee, confessed to receiving death threats and $20,000 during the 1990 Copa Libertadores match between Nacional and Vasco da Gama.

[29] In the 1991 Libertadores, Nacional were once again eliminated in the semi-finals by Olimpia, while in that same year they won their fifth Primera A title after placing first in the final round against América, Junior and Santa Fe.

In 2007, Nacional won both tournaments of the year: in the Apertura they beat Atlético Huila, and in the Finalización, they defeated La Equidad in the finals.

The team also won its second Copa Colombia title defeating Millonarios with an aggregate score of 3–2, completing a domestic double in the process.

However they came back in dramatic fashion in the second leg; with the score tied at 1–1 Junior was just minutes away from lifting the Colombian title, but a goal from Jhon Valoy in the 94th minute sent the game to penalties, where Nacional won the shootout and lifted their third consecutive title, becoming the first Colombian club to win three consecutive short tournaments.

Nacional followed this championship with a good performance in the 2014 Copa Sudamericana, and although they were almost eliminated at the hands of Paraguayan minnows General Díaz in the second stage, they made the finals, where they faced River Plate.

The second leg, played in Buenos Aires, was won by River Plate with a 2–0 score, making this the second runner-up finish for the club after losing the final in 2002.

They qualified to the playoffs as the first seed and later beat crosstown rivals Independiente Medellín on their path to the finals, where they defeated Junior on penalties after a 2–2 draw on aggregate.

[36] In 2016, Nacional also won its third Copa Colombia title after beating Junior in the finals with an aggregate score of 3–1, becoming the most successful club in the tournament.

It was the first final in an international competition for the Brazilian side, who had eliminated Cuiabá, Independiente, Junior and San Lorenzo to reach that round.

[43] However, on 28 November, two days before the first leg, LaMia Flight 2933 crashed in Cerro Gordo, La Unión, just a few kilometres from Medellín, with the Chapecoense team on board.

[45] On the planned date of the match, Nacional and the City Council of Medellín organised a memorial to honor the victims of the tragedy.

[50] Nacional qualified to the 2016 FIFA Club World Cup as the champion of the 2016 Copa Libertadores, representing South America in the competition.

[51] Nacional got third place after beating CONCACAF Champions League winner Club América 4–3 on penalties after a 2–2 draw in regulation time.

[68][69] This match gained importance starting from the decade of the 1980s, when both América de Cali and Atlético Nacional began to stand out in local competition and continental tournaments.

The two teams have faced each other in final stages 15 times and have played five league title-deciders between them: in 1981, 1984, 1991, 1999, and the 2002 Apertura, with Nacional winning three of these (1981, 1991, 1999) and América the remaining two.

The badge consists of a rectangle elongated downward, with the initials A and N inside, and the tower of a castle above symbolizing "grandeur, tradition, strength and hierarchy", similar to the city's coat of arms.

Atlético Nacional's women's team was founded as a youth academy on 25 August 2009, with the project being led by Diego Bedoya as manager and supported by Víctor Marulanda.