This study aims to investigate how online collaboration can support the learning of science, technology, engineering, and mathematics (STEM) in higher education. Empirical data were collected from 88 postgraduate students studying at the African Centre of Excellence for Innovative Teaching Learning Mathematics and Science (ACEITLMS) using online oral interviews and two five-point Likert scale questionnaires. Interviews were analysed through content analysis while data from the questionnaire were scanned through the Statistical Package for Social Scientists (SPSS) to compute descriptive statistics and Spearman rho correlation coefficient. The findings indicate that online collaborative learning through small group discussions prompt knowledge co-construction, and higher-order thinking skills in STEM subjects. Moreover, the findings demonstrate how several electronic multimedia tools (PhET simulations, animations, YouTube videos) can increase student retention and engagement in learning STEM. Though the students reported that they experienced challenges such as poor internet connection, lack of laboratory work, electricity shortage, and limited ICT skills, they managed to complete STEM learning activities by using free virtual laboratories, portable tethering hotspots from their smartphones, and smartphones where power was a problem and learnt the navigation of ICT tools from their peers. The study found moderate positive Spearman rho correlation coefficient, which explains that 69% of the total variance in the students’ successful performance is explained by the two variables, i.e., social and cognitive presence. The study recommends more training for course instructors and students. Efforts should be put in place to focus on ICT manipulation and curating interactive content. The researchers acclaim the expansion of internet coverage in University of Rwanda campuses. This action will enhance online and blended learning. Moreover, the study recommends the integration of ICT and the use of multimedia tools such as Bio-interactive and Physics Education Technology (PhET) interactive simulations in STEM subjects as supplementary resources. These tools support cognitive and affective domains in the teaching and learning process. Furthermore, universities can reduce the problem of expensive and inadequate laboratory equipment by adopting the use of virtual laboratories, especially for online STEM lessons.

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