Seed saving is crucial to ensure seed and food security, especially in developing countries. In Ghana, about 90% of pearl millet farmers utilise farmer-saved seed for production. Such seeds usually have a low germination rate, and may carry important seed-borne pathogens. In this study, the quality of farmer-saved seeds and the potential of botanicals to control seed-borne fungi were examined. A structured questionnaire was administered to 120 farmers from Garu, Bongo and Kassana-Nankana districts in Ghana. During the survey, 60 samples of farmer-saved seed were obtained for seed quality evaluation. Aqueous extracts of neem (Azadirachta indica) and citrus (Citrus sinensis) were prepared as seed treatments compared with a control. Fourteen (14) fungal species were associated with the seed samples, but the four dominant ones were Curvularia spp. (62%), Talaromyces spp. (53%), Aspergillus spp. (52%) and Exserohilum spp. (42%). The application of citrus extract inhibited fungal incidence (15–31.7%) compared to neem extract (33.3–93.3%) and the control (96.7–98.3%). The application of citrus extract resulted in a higher (74.7–82.8%) field germination rate compared to neem extract (62.3–73.2%) and the control (65.5–69.2%). The citrus extract was the most efficient treatment in reducing the incidence of fungi and enhancing the seed germination and vigour of pearl millet.