Meyer played an important role in Natal during the Second Anglo-Boer War as General of the southern commandos in the Transvaal and the various advances into Natal. He commanded the Boer forces attacking Dundee at the Battle of Talana Hill on 20 October 1899. However, due to illness, he was forced to leave the scene of fighting during the battle at Modderspruit on 30 October 1899 and command was taken over by General Louis Botha. Meyer returned to the battlefield and took part in the Battle of Vaal Krantz during February 1900 and also assisted with the occupation of Biggarsberg in May 1900.