Seed-borne fungal pathogens present significant constrain to the production and conservation of many seed crops including cowpea. Infection of mature seeds by such pathogens could result in mycotoxin contamination, loss of viability, and decay of seeds. This study aimed to identify seed-borne fungi on 200 accessions of cowpea under cold storage at CSIR-Plant Genetic Resources Research Institute (PGRRI), Ghana. Also, the antifungal effect of seeds of Piper nigrum, Xylopia aethiopica, Aframomum melegueta, and fresh leaves of Cymbopogon citratus aqueous extracts (100% w/v) on the major seed-borne fungi identified on the cowpea seeds was determined. Seven fungal species belonging to five genera were identified from the seeds of the cowpea accessions evaluated. However, the diversity and infection levels of the pathogenic fungi recorded on the seeds were lower than that of the saprophytic fungi indicating minimal capacity of the seeds to spread pathogenic fungi on the field. Aqueous extract of Aframomum melegueta inhibited the growth of Fusarium verticillioides by 98.40%, Colletotrichum sp. by 97.83%, Aspergillus niger by 94.70%, and Aspergillus flavus by 63.38%. The only other aqueous extract that inhibited the colony growth above 60% was that of Piper nigrum which inhibited colony growth of Fusarium verticillioides by 71.7% and Colletotrichum sp. by 63.47%. Due to the benign effect of Aframomum melegueta extract on the environment and non-target organisms, its use as a seed protectant is highly recommended. Further studies to establish the spectrum of activity and dose levels of Aframomum melegueta extract are recommended.