Crop yield is a derivative of the number of plants harvested. In Ghana, soybean fields are mostly sparsely populated with less than the optimum number of plants, a phenomenon that contributes to poor yields of only 46% of the crop’s potential in farmers’ fields. The low plant population could be the result of the poor quality of the seed planted. Meanwhile, the quality of seed is determined by crop production practices, the environmental conditions of the mother plant, and postharvest handling technologies used. Over 90% of the country’s soybean seed comes from the northern part of Ghana, predominantly the Guinea Savannah. In this study, seed lots of soybean genotypes produced within the Savanna Agroecological Zone of Ghana, were evaluated for physical and physiological traits, and the prevalence of seed borne fungi. Results showed that seed lots produced within the zone and stored under ambient conditions have medium-sized (100 to 140 g/1000 seeds) seeds with an average seed weight of 133 g/1000 seeds. The seed lots evaluated had physical purity values higher than the minimum certification standard of 98% for soybean seed in Ghana. Wrinkled seeds were the most dominant component of the seed with visual defects followed closely by seeds that were discoloured, cracked, and those with purple stains. Aspergillus flavus, Aspergillus niger, Chaetomium globosum, Rhizopus sp and Macrophomina phaseolina were the main fungi identified. Furthermore, the seed lots had an average germination percentage of 86%, which is within the acceptable minimum certification standards for soybean seed in Ghana. Though germination and vigour were variable among the seed lots tested, these parameters were not affected by the presence of the fungi species identified and the amount of seed with visual defects. The findings of this study strongly suggest that the low plant density and the resultant poor yields of soybean usually recorded in farmers’ fields in Ghana are likely due to suboptimal seeding rates at planting coupled with the low use of good agronomic practices with only a small fraction attributable to poor seed quality