Gardner became a Member of Parliament for Plymouth in 1790 and later for Westminster in 1796. He was appointed to the Board of Admiralty in 1790 and was appointed commander-in-chief of the Leeward Islands Station in 1793. As rear admiral in November 1793, he was among the first officers to articulate a growing conviction in the navy that lemons were the best cure for scurvy and, going against prevailing medical opinion, demanded a supply for his ships. The resulting scurvy-free voyage of to India was a crucial element in the Admiralty's decision in 1795 to issue lemon juice as a daily ration in the navy – a policy which drastically minimised outbreaks of scurvy. He left the Admiralty Board in 1795 and was promoted to full admiral. He commanded a squadron during the Mutiny at Spithead in 1797, and Gardner negotiated directly with the mutineers, until he lost his temper, seized a mutineer by the throat and threatened to hang the lot. This nearly led to his own demise at the hands of the mutineers, but cooler heads prevailed.