After the English invaded South Africa in 1899, Duquesne returned to South Africa to join the Boer commandos as a lieutenant attached to the staff of Commandant General Piet Joubert in Pretoria. He was wounded with a bullet through his right shoulder at the Siege of Ladysmith, but was promoted to the rank of captain in the artillery. Duquesne was captured by the English at the Battle of Colenso, but escaped in Durban.