A fundamental ecological impact of climate change is the alteration of agroecosystems. In particular, soil-pathogen levels and crop health are important as they eventually influence food security. The aim of this short scoping review synthesis focusing on recent updated research (last 5 years) is to better understand the link between climatic factors such as temperature, precipitation, and soil moisture, and their direct and indirect impacts on the distribution and proliferation of pathogens affecting crop yield and food security. The observed outcome of the synthesis was that increase in soil pathogen levels and the resulting decrease in crop yield, coupled with heightened risk levels of mycotoxin contamination requires urgent need for adaptive strategies to safeguard global food systems in the face of anthropogenic climate change.