 After serving as adjutant to Governor Arthur Phillip, Johnston served in the New South Wales Corps and he was a key figure in putting down the Castle Hill convict rebellion in 1804.He led his troops in deposing Governor Bligh in the Rum Rebellion in 1808; which led to his court martial and subsequent cashiering from military service.In his later life, he returned to New South Wales as a private citizen, raising a family in the colony and establishing a successful farm around Annandale in Sydney.