Col Jonathan Ngwenya received his basic military training as APLA activist in Conakry, Guinea in 1977. He completed his Instructor Course at Kwame Nkrumah Military Base. In 1978, he was deployed to the APLA headquarters in Dar-es-Salaam, Tanzania.
Between 1978 and 1983 Ngwenya served as APLA Platoon and Company Commander respectively. He served in the Operational Directive of APLA in Tanzania, Zimbabwe and Botswana until 1994, after which he was integrated into the South African National Defence Force (SANDF) as a major and appointed as an SO2 Counter Intelligence Officer.
As a member of the SANDF, Ngwenya completed all bridging training courses and was promoted to the rank of Lieutenant Colonel as SO1 Foreign Training within the Defence Foreign Relations environment until 2003. In 2004, he completed his joint Senior Commandand Staff Programme and later joined the Directing Staff at the South African National War College for a short while.
Ngwenya enjoys reading and running. He is married to Martha and they have two children, Lindiwe and Mpho.