Burgoyne returned to Portugal in April 1809 to join Sir Arthur Wellesley's army. Promoted to captain on 5 July 1809, Burgoyne became engineer officer for the 3rd Division, in which role he took part in the Battle of Bussaco in September 1810, the Second Siege of Badajoz in June 1811 and the Siege of Ciudad Rodrigo in January 1812. Promoted to brevet major on 6 February 1812, he led the storming parties at the Siege of Badajoz in March 1812. Promoted again this time to brevet lieutenant colonel on 27 April 1812, he took part in the Battle of Salamanca in July 1812, the Siege of Burgos in September 1812 and the Battle of Vitoria in June 1813 before going on to be present at the Siege of San Sebastián in August 1813, the Battle of Nivelle in November 1813 and the Battle of the Nive in December 1813. In the closing stages of the War he was also present at the crossing of the River Adour in February 1814 and the Battle of Bayonne in April 1814. He was appointed a Companion of the Order of the Bath in 1814.