In 1840 Barry was posted to the Leeward Islands and Windward Islands of the West Indies, there focusing on medicine, management and improving the conditions of the troops, and receiving a promotion to Principal Medical Officer. In 1845, Barry contracted yellow fever and left for England for sick leave in October. After being cleared for duty, Barry was posted to Malta in 1846. Here Barry was severely reprimanded for inexplicably taking a seat in the local church that was reserved for the clergy, and had to deal with the threat – and eventual actuality – of a cholera epidemic, which broke out in 1850.