Makhafola is currently the General Manager Research and Development at Mintek. He worked as Lecturer in Analytical Chemistry at Tshwane University of Technology and University of Venda. In 2004 was appointed Director: Quality Assurance at Walter Sisulu University). Dr Makhafola was the Director: Quality Assurance at the University of Venda until he joined University of Kwa-Zulu Natal as the Director Quality Promotion & Assurance in July 2010, part of his responsibility was to lead the World University Rankings project. Dr Makhafola served as member of various boards and committees. He is currently the Chairperson of DST/MINTEK NIC Steering Committee. He did the post-doctoral training at Indiana University and presented his research work in more than 19 international conferences and published in credible journals.