He coached Mohammedan Sporting Club during the 2006 season, but was not as successful there as he was during his stint with East Bengal. In 2007, a relegation threatened Salgaocar SC appointed Subhash Bhowmick to be their technical director. He remained as the Technical Director of the Goan outfit for the 2008 season also. Towards the end of the 2008-09 I-League, a relegation threatened East Bengal Club appointed Bhowmick as their coach. He was retained as coach for the 2009-10 season, a particularly dismal season for the club. East Bengal lost all the matches they played, most of them against smaller clubs, in both the IFA Shield as well as the Durand Cup. Supporters and club officials fixed the blame squarely on Bhowmick, as he was essentially the only man responsible for team making and pre-season training for the 2009-10 season. Despite significant autonomy granted to Bhowmick by East Bengal administrators, as well as provision of extra training facilities, his team failed to perform.