A nationwide survey was performed to study the distribution of parasites, pathogens and pesticides in managed honey bee populations in Ghana. When 45 colonies were sampled and inspected for signs of disease, Varroa destructor was the most prevalent parasite (89%; n = 40), all mites corresponding to the Korean haplotype of this pathogen. Aethina tumida (42%; n = 19) and Braula coeca (7%; n = 3) were also detected, as were Melissococcus plutonius and trypanosomatids (7%). By contrast, Nosema spp., Acarapis spp., Ascosphaera apis and Paenibacillus larvae were not detected by molecular screening. Amitraz was the most widely distributed pesticide (75%; n = 23) followed by coumaphos (47%; n = 15), chlorpyrifos (34%; n = 15) and fluvalinate (31%; n = 10). This survey lays the groundwork for further monitoring of honey bee populations in Ghana.