Glaciers are receding at an unprecedented rate with expected losses of up to half their masses by 2100. Such changes will have a profound effect on the physicochemical characteristics of glacier-fed stream (GFS) water, such as the composition of organic matter, turbidity, conductivity, and patterns in discharge. Hence, direct effects are anticipated for the microbial communities and assemblages inhabiting these environments. High-elevation tropical glaciers are already responding to these enhanced changes (e.g. temperature) and thus are a proxy to study the ecology of GFSs in the future. Here, we sampled and studied the Mt Stanley glacier in Africa’s ‘Mountains of the Moon’ (Rwenzori National Park, Uganda). We showed that the benthic microbiome from this GFS is distinct at several levels from other GFSs worldwide. Specifically, several novel taxa were present, and usually, common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while >80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.