This research examines the strengths, weaknesses, opportunities and threats (SWOT) to integrating e-learning perceived by academic staff at a university in Uganda and a university in Tanzania. Mixed-methods research was used in which a main qualitative study was complemented by a quantitative method. The sample participants were academic staff from Mountains of the Moon University in Uganda (n = 20) and Mzumbe University in Tanzania (n = 20). The SWOTs from three aspects are analysed: institution-related, instruction-related and investment-related aspects. The results show that at both universities the institutions and teachers understand the need to integrate e-learning, which provides strengths and opportunities for the universities; however, the lack of capacities in terms of institutional policies, teacher competences and internal investment constitutes the weaknesses and threats for the universities.