Cubbon arrived in India earlier than required in the summer of 1801 at Calcutta. He gained an appointment to the 2nd Madras Battalion in 1802, and moved to the 2nd Battalion 5th Native Infantry in July 1804, serving in Travancore under Col. John Chalmers. Cubbon had great admiration for the Sepoys and respected their religious views. In 1809 he received a civil appointment but the new governor of Madras, George Barlow, had passed a pledge that was unpopular among the Europeans in the Madras Army. Cubbon refused to sign the declaration and he lost his appointment during this so-called white mutiny in Madras. He was reappointed in 1810 in the Commissariat Department initially under Col. Close in central India during the Pindari War and then under Colonel Philip Meadows Taylor in Kurnool. A year later, he was then made an Assistant Commissary-General, a position well above the ranks within the army. He became a Major on 23 November 1823 and was a Lieutenant-Colonel on 22 April 1826. In 1827 he moved south to serve under the Travancore Resident as Commissary-General, succeeding William Morrison.