Until the disfunction of its senior team in June 2023, Salgaocar competed in the Goa Professional League.

[2] Salgaocar previously competed in the I-League,[3] then top-flight of the Indian football league system.

[14] They became the first Goan side to win the National Football League, under the guidance of coach Shabbir Ali.

[18] Salgaocar pulled out of the I-League in 2017, citing the All India Football Federation (AIFF) bias.

In 1988, they clinched Sait Nagjee Cup in Kerala; In 1989, the reached final again, but ended-up as runners-up after being defeated to Bangladeshi club Dhaka Abahani.

[33][34] Salgaocar participated in the National Football League (India) since the tournament began in 1996,[35][36][37] and successfully annexed all possible trophies on the Indian circuit thereby etching their name amongst the top teams in the country.

Critics have been swift in writing the club off, but managed to make the first division of the NFL in 2003 and staying their till the beginning of the I-League.

[47] In the 2002–03 National Football League season, Salgaocar achieved success and they earned runners-up position,[48] after ending their journey with 44 points in 22 matches.

[57][58] In the 2010–11 season, Salgaocar played in the I-League which was India's biggest football competition and they emerged as the champions.

[60] On 29 September 2011, Salgaocar won their second trophy in four months by winning the 2011 Indian Federation Cup by beating East Bengal in the Final 3–1.

[65][66][67] His one-year contract was terminated before the end of the year, due to poor performances and prolonged national team duties.

[73] Salgaocar replaced Booth with Derrick Pereira who had been the coach of Pune FC for the past four seasons and had led them to two consecutive top-5 finishes in the I-League.

[74][75] In 2014 Durand Cup, held from 20 October to 8 November in Goa, Salgaocar emerged championship defeating Pune FC 1–0 in final.

[85][86][87][88][89] In September 2012, Salgaocar unveiled new club crest, different from the previous one, with having symbol of glory, mining tools highlighting the foundation of the V. M. Salgaocar Group, a conch symbolising new hope and an auspicious beginning, and a ribbon with fire indicating pride and passion.

[187] In December 2008, Salgaocar U-15 side defeated Raghav Football Club of Gurgaon 2–0 to win the India leg of the fourth (Under-15) Manchester United Premier Cup and earned the right to represent the country in the world finals in Manchester, England.