Independiente Santa Fe was officially founded on February 28, 1941, as an amateur football team. The club's founders were mainly graduates from the
Gimnasio Moderno and of a high social class. Santa Fe was at first going to be a team based on ex-students of Gimnasio Moderno, but later incorporated players from other schools. The primary objective of the club was to participate in a local tournament hosted by the Sports Association of Bogotá. Their first recorded game was against Universal, a match that ended in a goalless draw. The team ended the tournament as runner-up with 20 points, being beaten by Legión Militar Deportiva de los Taxis Rojos, a representative of a transportation company. In 1942, Santa Fe was coached by
Jack Greenwell, former
Barcelona player and coach, notable for having won three times the
Copa del Rey and the
1939 South American Championship with
Peru. That year Santa Fe played in the first division of the A.D.B., which was canceled in the middle of that year. That same year also reached the final of the
Torneo de Cundinamarca, which lost against
América de Cali. Jack Greenwell died on November 20 of that year. On 21 May 1948 the
DIMAYOR was established in Colombia, which would serve to manage Colombian professional football. They agreed to hold the
first professional championship for the second half of the year. On August 15, Santa Fe played its first game in the professional championship against
Deportes Caldas, a match that ended 3–3. Santa Fe finished the league as the first champion of the
Colombian first division, winning 12 of 18 games, drew 3 and also lost 3. The team was able to score 57 goals for and received 29 goals. The goalscorer of the team was the
Spanish Argentine Jesús María Lires with 20 goals, second goalscorer of the tournament. Next year Santa Fe was third, five points behind the champion, local rivals
Millonarios. Seeking for a new title, Santa Fe took advantage of the events of
El Dorado signing Argentines
Héctor Rial and
René Pontoni (the former became a star of
Real Madrid years later), as well the Englishmen
Neil Franklin and
George Mountford from
Stoke City, and
Charlie Mitten from
Manchester United. However, the signings did little, as Santa Fe was not into the top three for about ten years, being their worst the
1954 campaign where they finished last with just five points. In 1958, Santa Fe got its second title after finishing first with 48 points. They got its third title just two after years with 61 points. Getting this title, Santa Fe became the second Colombian club appearing at the
Copa Libertadores. In that tournament, Santa Fe was placed in the preliminary round with Ecuadorian club
Barcelona. The first match was a 3–0 victory for Santa Fe and the second game was a 2–2 draw. In the next round, Santa Fe eliminated Bolivian
club Jorge Wilstermann. Santa Fe drew 2–2 with Jorge Wilstermann on point aggregate and 3–3 on aggregate score, so the winner was decided by a draw of lots. In the semifinals, Santa Fe faced Brazilian club
Palmeiras. The home leg was a 2–2 draw, but Santa Fe lost 4–1 in the away leg. Santa Fe's first success in the 2000s came late, when the team won the
Copa Colombia, beating
Deportivo Pasto in the finals. Since then, Santa Fe has had a successful period. Santa Fe got its seventh league title in the
2012 Torneo Apertura, 37 years after its last league title. Santa Fe was second in the First Stage of the tournament with 29 points. In the semifinals, they were grouped with
Boyacá Chicó,
Itagüí and
La Equidad. Santa Fe advanced to the finals with 14 points. Santa Fe faced
Deportivo Pasto in the finals. The first match ended in a 1–1 draw and the second was a 1–0 victory for Santa Fe. They got its first
Superliga Colombiana title the next year and were runners-up in the
2013 Torneo Apertura, won by
Atlético Nacional. In its
Copa Libertadores appearance, they got into Semifinals. They began the tournament in the Second Stage, facing
Cerro Porteño,
Deportes Tolima and
Real Garcilaso, where they finished first with 14 points and unbeaten. They eliminated
Grêmio in the Round of 16 and Real Garcilaso in the quarterfinals. In the semifinals, they were eliminated by
Olimpia, with an aggregate score of 2–1. In the
2014 Torneo Apertura, Santa Fe was fourth on the First Stage, advancing to Quarterfinals. There Santa Fe eliminated
Once Caldas with an aggregate score of 5–3. In the semifinals, the team faced
Atlético Nacional. The first match ended in a 1–0 win for Santa Fe. However, Nacional got a comeback with a 2–0 win, thus eliminating Santa Fe. In the Torneo Finalización, Santa Fe was first with 31 points. In the semifinals, the team was placed in a group with
Atlético Huila, Atlético Nacional and
Once Caldas. Santa Fe placed first in the group, advancing to the finals where they faced
Independiente Medellín. Santa Fe won the first match and drew in the second, with an aggregate score of 3–2, winning its 8th title. That year, Santa Fe was runner-up in the
Copa Colombia, losing the finals against
Deportes Tolima with an aggregate score of 3–2. In the
2014 Copa Libertadores, Santa Fe played against
Monarcas Morelia in the First Stage, drawing 2–2 on aggregate score and advancing to the next round due to
away goals rule. In the Second Stage, the team was last of its group, in which they faced
Atlético Mineiro,
Club Nacional and
Zamora, winning only one match of six. The
2015 season had a great start for the team, as they qualified for the
2015 Copa Sudamericana after winning
2015 Superliga Colombiana in which they faced 2014 Torneo Apertura winners
Atlético Nacional. However, in the 2015 Torneo Apertura, the team can not advance to the knockout phase after placing ninth with 31 points. In the Torneo Finalización, the team was 8th with the same number of points as the last tournament, however this time it was enough to advance to the next round. There the team was eliminated by
Junior, whom also defeated them months later in the
Copa Colombia Finals. The international season of the team began with its
Copa Libertadores participation. The team started in the Second Stage, where they faced
Atlético Mineiro,
Colo-Colo and
Club Atlas. Santa Fe placed 1st with 12 points. In the Round of 16, they played against Argentine team
Estudiantes de La Plata. They lost the away match 2–1, but with a 2–0 victory in home the team advanced to the quarterfinals. There the team faced Brazilian club
Internacional. The team got a 1–0 victory in the home game, but lost 2–0 in the away match. Santa Fe got its first international title in the
2015 Copa Sudamericana. They eliminated Ecuadorian
LDU Loja in the First Stage and Uruguayan
Nacional in the Second Stage. In the Round of 16 they eliminated Ecuadorian
Emelec on
away goals after drawing 2–2 on aggregate score. In the quarterfinals they won 2–1 on aggregate to Argentine
Independiente and in the semifinals they also advanced on away goals after drawing 1–1 with Paraguayan
Sportivo Luqueño. In the finals they faced Argentine
Huracán. After drawing 0–0 in both matches, the winner had to be decided on
penalties. There Santa Fe won 3–1, thus getting the first international title of the club and qualifying for the
2016 Copa Libertadores,
2016 Recopa Sudamericana and
2016 Suruga Bank Championship. Santa Fe's
Wilson Morelo tied with three footballers as top goalscorers of the tournament with five goals. In the
2016 Torneo Apertura, Santa Fe placed fourth, advancing to the next round. There, Santa Fe was eliminated by
Cortuluá with an aggregate score of 2–3. In the
2016 Copa Libertadores, the team advanced to the Second Stage after eliminate
Oriente Petrolero with an aggregate of 1–6. However, they were eliminated in the Second Stage after placing third in a group consisting of
Cerro Porteño,
Cobresal (who were last) and
Corinthians. In the
2025 Torneo Apertura, Santa Fe placed sixth, advancing to the semi-finals. After placing first in Group A, the team defeated
Independiente Medellín 2-1 in aggregate to win their tenth national title. ==Colours and badge==