In Sub-Saharan Africa, cereals are threatened by stress-inducing microbial pathogens and parasites such as fungi, bacteria, viruses and nematodes leading to significant losses. Mycotoxin-producing fungi like Fusarium graminearum induce head blight disease causing 30–70% of yield losses in wheat. In comparison, Fusarium verticillioides accounts for ear rot diseases that account for 13–70% of maize yield losses in Sub-Saharan Africa. Outbreaks of the devastating rice blast pathogen Magnaporthe oryzae have caused up to 48% yield losses of rice in Kenya. The grey leaf spot fungus, C. zeina, gradually becomes a threat to maize production, causing a 65% yield loss in South Africa. Maize smut and ergot-causing pathogens, Sporisorium ehrenbergii and Claviceps africana, under mildly humid and cold climatic conditions, impact grain quality and market value. The maize streak virus predominantly ravages maize fields all over Sub-Saharan Africa causing 30–100% yield losses while the diseases caused by the bacterium Xanthomonas oryzae pv. oryzae has led to 10 to 50% yield losses in rice production. In Nigeria, nematode pathogens like Pratylenchus spp have been reported to cause yield losses of up to 27% in maize production. This review fundamentally discusses these cereal pathogens and their current and future impact in the face of climate change in Africa. We seriously emphasize the need for more simulation studies on each of these pathogens across Sub-Saharan Africa and their potential impact under current and future climate change scenarios.