The COVID-19 pandemic restricted access to campuses of universities owing to intermittent lockdowns. Consequently, educational institutions were forced to adopt virtual teaching techniques to ensure continued teaching and learning. However, the effective implementation of online education in universities in Uganda faced capability challenges that hindered its effectiveness. Therefore, this study investigated the influence of universities’ capabilities on the effective implementation of e-learning in public universities in Kampala City, Uganda during and beyond the COVID-19 pandemic period. Anchoring in resource-based theory (RBT), universities’ capabilities for effective implementation e-learning studied included experimentation, integration capability, and content management. Using the quantitative approach, cross-sectional data was collected from a sample of 312 academic staff from Kyambogo and Makerere Universities, the only two public universities located in Kampala City, Uganda. Data was collected using a self-administered questionnaire. The data was analysed using descriptive and inferential statistics. Descriptive statistics involved the calculation of means while inferential analysis involved structural equation models (SEM) using SmartPLS. The results revealed that content management and integration capability positively and significantly predicted e-learning implementation. However, experimentation negatively and insignificantly predicted e-learning implementation. The study concluded that content management and integration capability are vital for e-learning implementation. Nonetheless, experimentation is not a probable requirement for the effective implementation of e-learning. Therefore, it was recommended that university managers should develop integration capabilities, and should support lecturers to improve their content management, but experimentation should not be prioritised in the implementation of e-learning.