The former full back arrived in Pune last week and has begun work on developing a well-rounded youth structure for the development and nurturing of young footballing talent present in the city, said a release from Bharat FC.
Knowles is a former professional footballer with more than 300 appearances to his credit for five clubs in England before becoming the coach of Wigan Athletic, where he enjoyed success as a player, at the age of 33.
Knowles is credited with spotting current England international Leighton Baines' potential.
His last assignment was as the head coach at Burnley College Football Academy.
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Amongst the first coaches in England to complete the UEFA A License, the 55-year-old Knowles has also worked with clubs like Ajax, Barcelona and Bayern Munich.
Bharat FC's MD Amit Kalyani said the appointment of Knowles was made keeping in mind the Englishman's proven work with young players and the ability to put in place holistic development programmes that ensure the all-round development of talented young footballers.
"Stuart has a great reputation in England and when he told me about the chance to come to India, I was really excited. My goal is to give Bharat FC the best youth system in this country," he said.
Bharat FC are currently in the process of constructing their own training ground at Manjr to house the club's academy, the release added.