October 1795 saw him made physician to the forces, accompanying Admiral Christian's fleet to Santo Domingo and being sent to Gibraltar in 1804 to treat a contagious fever outbreak there. In April 1806 he came back to England, where in 1809 George III knighted him and appointed him chief of the medical department of the army at Cadiz, then in the midst of the Peninsular War. He then became deputy inspector (March 1813) then inspector (April 1813) of hospitals before retiring on half pay in 1814. Having been a first-hand eyewitness of epidemics at Cadiz, Malaga and Gibraltar, he then published Reports of the pestilential disorder of Andalusia, which appeared at Cadiz in the years 1800, 1804, 1810, and 1813 (1815). Arthur Wellesley appointed Fellowes deputy county lieutenant for Hampshire and Mrs Piozzi left Fellowes her manuscripts and copies of her writings with handwritten notes in 1821, with Fellowes becoming her literary executor.