In January 1799 a second rebellion occurred in Graaff-Reinet necessitating the Third Frontier War. In March of the same year, Government of the First British Occupation sent some British soldiers under Gen T P Vandeleur to crush the Graaff-Reinet revolt. No sooner was this done (April 1799) than some discontented Khoikhoi revolted, joined with the Xhosa in the Zuurveld and began attacking white farms, reaching as far as Oudtshoorn by July 1799. Vandeleur's force on its way back to Algoa Bay was attacked by a Gqunukwebe clan, fearing expulsion from the Zuurveld.
Commandos from Graaff-Reinet and Swellendam were mustered, and a string of clashes ensued. The Government dreaded a general Khoi rising, and so made peace and allowed the Xhosas to remain in the Zuurveld. In 1801, another Graaff-Reinet rebellion began, forcing further Khoi desertions. Farms were abandoned en masse, and the Khoi bands under Klaas Stuurman, Hans Trompetter and Boesak carried out widespread raids.
Although several commandos took the field, including a Swellendam commando under Comdt Tjaart van der Walt, who was killed in action in June 1802, they achieved no permanent result. Even a 'great commando' assembled from Graaff-Reinet, Swellendam and Stellenbosch could not make any real headway. In February 1803, just before the British government handed over the Cape Administration to the Batavian Republic, and an inconclusive peace was arranged. The Batavian authorities propitiated the resentment of the eastern-frontier Khoi-khoi but could not persuade the Xhosas to leave the Zuurveld (1803-1806).