Year 2000, club touches the sky as it wins Sikkim Governor’s Gold Cup, All Airlines Gold Cup, Durand Cup, Rovers Cup and National Football League. The Magic of Mohun Bagan striker, Brazillian ball charmer Barreto (Jose Lui Ramirez Barreto) hypnotised the football fans of the country. Mohun Bagan adopted a news jersey this year, designed from United Kingdom. 2001 again was a very good year for the club.Mohun Bagan shows good performance as mariners won Kolkata Football League,Federation Cup, Sikkim Governor’s Gold Cup, Bardoloi Trophy and the National Football League. Barreto continued to show his excellence. In 2002, Baichung Bhutia came back home from England, and has been taken by Mohun Bagan. But the team got very little service from him, as Bhutia got injured early in the season, and could not play for Mariners anymore.This year Club saw Limited Success, but secired the All Airlines Gold Cup.

2003 was the year, in which Mariners virtually had no team at all. There was a change in coach this year, except Barreto, Renedy and Basudeb there were no good players in teh squad. And Barreto left for Malyasia for unknown reason. Although Mohun Bagan lifted IFA Shield by defeating East Bengal, but the performance of this year was not upto the mark.

2004 started with a depressed situation, when star player Barreto left India without showing any reason. Mohun Bagan performed very poorly at the national league. But at this moment of crisis, the general of many battles, coach Subrata Bhattacharya returned to the club, and take the control immediately. The team secured a position of the super division of the national league. With a moderate team in the new season, Mariners started to show good football. Bad luck is yet to leave Bagan, but the team reached all the finals of the trophies that it took part. That is a record in itself. After runners up for 4 times, Mohun Bagan won the All Airlines Gold Cup. Another record in this year is the 9 – 0 victory with the Renown Sports Club from Sri Lanaka in IFA Shiled. Most probably that is the highest margin victory of Mohun Bagan against a foreign team.

In 2004, the supporters of Mohun Bagan “MOHUNBAGAN CLUB.COM” launched their own website https://www.mohunbaganclub.com. This is first football club website in India which was crowdfunded by supporters. This team eventually helped to launch official website of Mohun Bagan AC. Mohun Bagan became the first Indian club to launch their official website. The new era has began when the fans have their own association as “Green and Maroon, a Group of Mohun Bagan Supporters”. As the social, cultural and sporting dimensions of the club grow and grow, Mohun Bagan will be considered to be most important multi-sport club in the world. Mariners is the only other club on the continent who is the member of the FIFA Club Task Force with Jubilio Iawata of Japan among the elite group of 12 clubs in the world. In 2004, Mohun Bagan became the first Indian club to launch a credit card in association with ICICI Bank. 

Internal problems related to clubs election and court invention made huge dent into clubs performance. The situation slowly subsiding, Mohun Bagan assembled a strong side in 2006 that included Barreto and Bhaichung’s return, along with a combative Brazilian midfielder Douglas Silva. The team was further bolstered with top Indian players like Sangram Mukherjee, Deepak Mondal as well as youngsters like Lalawmpuia Pachuau, Lalkamal Bhowmick and Sushil Kumar Singh. With the sudden resignation of coach Biswajit Bhattacharya, the Brazilian physio of the team, Robson Mattos was hastily promoted as the team’s coach. Bhutia and Sangram’s collective heroics led them to their 12th Federation Cup. While the 2006–07 league season did not go well with as many as three foreign coaches taking part during the campaign in the form of Robson Mattos and former players – Chima Okorie and Bernard Oparanozie. FIFA president Sepp Blatter came to Kolkata and attended Mohun Bagan’s won 2–1 Derby win on 15 April 2007. On Mohun Bagan Day, the club became the first in India to launch an official mascot which was a tiger named “Baggu”.

In 2007 Mohun Bagan sealed their first-ever Indian Super Cup with a 4–0 victory over the league champions Dempo, with Bhutia scoring a hattrick. In 2007–08 season, where NFL got rebranded as I-League, Brazilian coach Carlos Roberto Pereira took the reins of the team but failed to win any significant accolade. In 2008, Mohun Bagan players got the opportunity to play against German icon Oliver Kahn in his official testimonial match for Bayern Munich, which also featured Brazilian star Zé Roberto. The match was played on 27 May 2008 at Vivekananda Yuba Bharati Krirangan and finished with Bayern Munich comfortably winning by 3–0. The same year Argentine World Cup winner Diego Maradona paid a visit to the club tent during a tour to India.

The following season, Mohun Bagan appointed Moroccan coach Karim Bencherifa, who led the team to a record 10-match winning run in the league and a Federation Cup victory. Still, poor performance in his second league resulted in him being sacked midway through the 2009–10 season and putting Satyajit Chatterjee as the interim coach. The only highlight of his second campaign was the 5–3 Derby victory on 25 October 2009.

The other sections of the club (Cricket, Hockey,athletics and Tennis) have all achieved success both at domestic and international level. All these play with the full support of 7000 club members and more than 200 fan clubs around the world. Mohun Bagan Athletic Club can take only 7000 members. Only death and other types of termination of membership vacant a place for new member, and after a thorough scrutiny by the executive committee, a new membership of the club has been offered.