These datasets are for the analyses carried out in paper in Journal of Animal Ecology titled 'The distribution of covert natural enemies of a globally invasive crop pest, the fall armyworm, in Africa; enemy-release and spillover events.' The authors of the paper are Amy J. Withers, Annabel Rice, Jolanda de Boer, Philip Donkersley, Aislinn J. Pearson, Gilson Chipabika, Patrick Karangwa, Bellancile Uzayisenga, Benjamin A. Mensah, Samuel Adjei Mensah, Phillip Obed Yobe Nkunika, Donald Kachigamba, Judith A. Smith, Christopher M. Jones and Kenneth Wilson.

 Invasive species pose a significant threat to biodiversity and agriculture worldwide, and here we investigated the prevalence of natural enemies in fall armyworm (Spodoptera frugiperda) in Africa. This study aimed to identify which microbial pathogens are present in invasive fall armyworm, and determine the geographical, meteorological, and temporal variables that influence prevalence. Larval samples were screened from Malawi, Rwanda, Kenya, Zambia, Sudan, and Ghana for the presence of four different microbial natural enemies; two nucleopolyhedroviruses, Spodoptera frugiperda NPV (SfMNPV) and Spodoptera exempta NPV (SpexNPV); the fungal pathogen Metarhizium rileyi; and the bacterium Wolbachia. One dataset (ALL_diseaseprevalence_year_season) includes the results of this screening for all four microbial nartural enemies and sampling information, the other dataset (SfMNPVprevalence_weather_topographic_temporal_variables) includes the results for SfMNPV and sampling information alongside variables relating to temperature, rainfall, elevation, growing season and time since the fall armyworm first arrived in each country. These variables were used to investigate whether SfMNPV prevalence was affected by geographical, meteorological or temporal variables.