After retiring as a footballer in 1985, Ali became a coach. He earned a first class diploma from the
Sports Authority of India. He successfully passed the German football association B License coach and also their four-week coaching course, which is equivalent to A License. Between 1997 and 1999, Ali managed top Goan outfit
Salgaocar and established himself as India's best coach. Barring a few like PK Banerjee and Syed Nayeemuddin, no other coach in India could win so many titles in such a short span as Ali did. Next Salgaocar won the
National League title, the only time a Goan team could win it till date. Ali then took the team to Bombay and won the Rovers Cup. Thereafter, the team flew into Delhi to bag the Durand Cup beating both Mohun Bagan and East Bengal and then tamed Mohun Bagan again in the Super Cup contest. No other teams in India have been given such a great run in Indian football in recent years. In 2006, he succeeded Mridul Banerjee as manager of another NFL side
Vasco. In 2008, he was again appointment head coach of Mohammedan. On 2 September 2022, he was unanimously appointed as the chairman of the
All India Football Federation Advisory Committee. He is also included in the board of eminent players of the AIFF. ==Football academy==