In 1962, Nanyemba left Namibia to join other SWAPO leaders abroad in Dar-es-Salaam, Tanzania. He quickly rose through the ranks and was appointed as Chief Representative for SWAPO in Botswana in 1963. He was recalled back to Tanzania in 1964 to serve as Chief Representative for East Africa, a position he held until 1969. During the controversial SWAPO Tanga Consultative Conference that took place between 1969 and 1970, Nanyemba was elected SWAPO Secretary of Defence, a crucial position at the time as the struggle for independence was getting more intense.

Following the collapse of the Portuguese colonial empire in Africa in 1974 thousands of young Namibians fled the country via Angola to join SWAPO and thus swelled the ranks of PLAN. It was at this stage of the struggle that Nanyemba began to play an important role in developing and organising PLAN into a real guerrilla fighting force. He was instrumental in arranging training and equipping PLAN. Under his leadership in 1977, the Swapo Military Council was reconstituted as the highest decision-making body of PLAN. He became the first chairman of the military council and chaired it until 1982, when Sam Nujoma as commander in chief took over. In 1977, with the help of the Soviet military advisers he established the Tobias Hainyeko Training Centre (THTC) in Lubango.

The four military regions, Eastern, North Eastern, Northern and North Western, were created under his leadership in 1977. He help set up another training centre, Jumbo Training Centre (JTC), west of Lubango in 1978. In 1979, under his supervision, the Operational Command Headquarters (OCHQ) was established. This was the headquarter of PLAN. Nanyemba had many achievements with PLAN under his leadership as SWAPO Secretary for Defence making PLAN the effective and efficient fighting machine it was.