During his career he served with distinction in various capacities in Maharashtra and Gujarat.

He was secretary to the then chief minister of Maharashtra, Vasantrao Naik, and Commissioner of the Brihanmumbai Municipal Corporation, Bombay.

B. G. Deshmukh was appointed as the 17th Cabinet Secretary of the Government of India in 1986, taking over from his batchmate P. K. Kaul, IAS (1951 UP).

In 1989, Rajiv Gandhi appointed him as his principal secretary, a post he went on to hold even under V.P.

He is also associated with social and development organisations such as Bombay Natural History Society, KEM Hospital, National Association for the Blind among others.