[3] He was present at the battles of Mudki, Ferozeshah, and Sobraon in 1845–46, where his superior Major George Broadfoot was killed and at the close of the Sikh campaign he was placed in charge of a new province in the Punjab.
There he filled in succession every office in the judicial and revenue departments across Punjab, and was rapidly promoted until 1867, when he resigned and returned to England, after having been a member of the Viceroy's Legislative Council and Home Secretary to the Government of India in 1864–65.
Cust returned to India and served in Lahore at the request of Sir John Lawrence but left again for England when his first wife died on 17 January 1864.
In 1867 his second wife died in childbirth and he decided to retire from Indian service even though he was just nine months away from completing the tenure needed to receive a full pension.
[3] After retiring to England Cust devoted himself to scientific research, philanthropy, and magisterial and municipal duties, declining reappointments in India.