During his coaching career, he managed all three
Kolkata-giants East Bengal,
Mohun Bagan and
Mohammedan Sporting. He took charge of Mohun Bagan first in 2000 when the club was undergoing a period of transition, and signed few notable foreigners including
Igor Shkvyrin from Uzbekistan,
Sammy Omollo from Kenya, and
Dusit Chalermsan from Thailand. He was sacked by the club in April 2003 after he was accused of having instigated some players of the team not to wear the Mohun Bagan jersey for the remaining two
National Football League matches as they were yet to get full payment. In 2007, Bhattacharya was appointed head coach of
East Bengal, but after their poor showing in the inaugural
2007–08 I-League, he resigned. He also managed then
NFL side
Tollygunge Agragami in 2003. He later served as both coach and technical director of
Prayag United (then known as Chirag United). Bhattacharya also managed ONGC in I-League. In 2015, Bhattacharya fought against
Satyajit Chatterjee for the post of football secretary in Mohun Bagan club election and was defeated by more than 2000 votes. In May 2018, it was officially announced that Bhattacharya was appointed head coach of another Kolkata based club
Bhawanipore. After unveiled new coach, he quoted "I am joining Bhawanipore instead of
Tollygunge Agragami. They are offering me a better package so I decided to join them. The management has agreed that the team would practice in
Kalyani instead of
Kolkata. So from the first week of June, we will start preparing for the season in Kalyani." In 2019, he joined Mohammedan Sporting as technical director. ==Personal life==