Fletcher was again mentioned in dispatches when serving as chief engineer at the second siege of Badajoz (19 May – 10 June 1811). The engineers suffered many casualties in their attempts to dig the thin rocky soils around a fort that had been repaired and reinforced since the last unsuccessful siege. Running short of ammunition and having sustained heavy losses; and with news that French reinforcements were on the way, Wellington withdrew his forces to Elvas on 10 June. Fletcher was also present when Ciudad Rodrigo (7 – 19 January 1812) and, on the third attempt, Badajoz (17 March – 16 April 1812) were captured. In the latter engagement it was Fletcher who identified the weak point in the defences and so ultimately decided where the main attack should be. On 19 March, Fletcher was shot in the groin when a French sortie in the fog reached the trenches where he and his engineers were working. His injury might have been much worse if it had not been for a Spanish Silver Dollar in his pocket which took the main force of the musket ball. Fletcher's injury had him confined to his tent where Wellington, desperately short of good engineers, visited him daily for advice. Fletcher returned to England to recover, and was made a baronet on 14 December 1812, and awarded a pension of £1.00 per diem. He received the Portuguese award of the Order of the Tower and Sword; and the Army Gold Cross for Talavera, Bussaco, Ciudad Rodrigo, and Badajoz.