He arrived in South Africa after the outbreak of the Second Boer War in late 1899 as Director of Supplies, serving in the 1899 operations in Natal, at the Relief of Ladysmith and in the battles of Colenso, Vaal Kranz, Tugela Heights, Pieters Hill, Laing’s Nek and Belfast. For his service he received a further four mentions in despatches, was promoted to the brevet rank of lieutenant-colonel on 29 November 1900, and was created a Companion of the Order of the Bath (CB) in the October 1902 South Africa Honours list. While in South Africa, he had three of his horses riding to victory in the inaugural meeting at Pretoria's new racecourse After the end of the war in June 1902, Morgan stayed in South Africa for several months, returning home on the SS "Scot" in November. In 1905 he was promoted to the substantial rank of lieutenant-colonel.