Although he had been in wretched health for months on end, Wallis had achieved much that helped shape Cook's Endeavour voyage. While there may or may not have been any direct contact between Wallis and Cook in the summer of 1768 many of the measures Cook employed to keep his crews healthy had been put into practice by Wallis.
While there had been debilitating outbreaks of scurvy aboard the Dolphin, there were no fatalities from the disease, and the mortality rate on the twenty-one-month voyage was remarkably low, with two deaths caused by accidents, and three due to malaria and dysentery.
Still, Wallis took a long time to recover from the voyage and in February 1770 he told the Admiralty he was still enduring bouts of ill health. The Board awarded him a gratuity of £525. Then, in November 1770, he was given command of the 74-gun third rate Torbay, and later of the 98-gun second rate Queen (October 1780)
Wallis also served as extra commissioner of the navy from 1782 to 1783, with a second term from 1787 until his death at home in London in January 1795.