The study was carried out to enumerate fungal contamination, and toxigenicity of Aspergillus flavus strains on cacao beans during drying and storage. As many as 3500 g cacao beans during drying and storage were purchased from smallholder farmers on the plantation areas at Karo Regency, Northern Sumatera. The percentage of the beans contaminated by fungi was conducted using direct plating. Fungal populations on soil and beans were determined using dilution followed by pour plated in dichloran 18% glycerol agar (DG18) and Aspergillus flavus and parasiticus agar (AFPA). The mycological evaluation was carried out based on morphological characteristics. Results showed eighteen genera of soil fungi were isolated at the cacao plantation; genera of Aspergillus sp., A. niger, A. flavus, and Penicillium citrinum were the most important contaminants. Six species of the fungi were associated with contamination on cocoa beans during drying i.e. Aspergillus sp., Candida tropicalis, Saccharomyces sp., A. niger, Penicillium spp., and Fusarium spp. Whereas three fungal species were associated during storage i.e. A. niger, A. flavus, and P. citrinum. The percentage of cacao contaminated during drying and storage was dominated (>40%) by Aspergillus sp. Fusarium sp. A. niger, A. flavus, and P. citrinum, respectively. Among 21 strains of A. flavus, 3 strains (15%) were isolated from soil, and 18 strains (85%) were isolated from beans during storage. Among toxigenic A. flavus, both strain scaf6 isolated from soil and strain cbaf5 isolated from beans during storage were the highest aflatoxin producers (30.0 ppb). Preventing soil contamination during harvesting, drying, and storage of cacao beans was a prerequisite to minimise fungal contamination.