Prediabetes is an important risk factor for the development of type 2 diabetes and is common in Nigeria. Effective intervention can reverse the underlying pathogenesis of pancreatic beta-cell dysfunction in prediabetes. Several studies have reported the prevalence of prediabetes across Nigeria, but lack information on the effect of intervention or natural outcome on pancreatic beta-cell function among Nigerians with prediabetes. The objective of this study was to determine and compare the effect of moderate exercise and metformin on pancreatic beta-cell function among participants with prediabetes. Using a randomized placebo-controlled design, fifty-four Nigerians with prediabetes were selected using simple random sampling. They were offered treatment with metformin, moderate exercise, or placebo and followed up for 12 weeks. Pancreatic beta-cell function was assessed before and after the interventions, and the outcome was compared. Forty-nine participants with prediabetes completed the study. After 12 weeks of intervention, participants in both the exercise and metformin groups had an increase in pancreatic beta-cell function compared to placebo. However, the exercise group had a greater increase in beta-cell function from the baseline with HOMA-B=61.9 (CI=-4.3±141.5) compared to 57.1(CI=-4.3±141.5) in the metformin group (p-value<0.05). Among Nigerians with prediabetes, moderate exercise and metformin interventions compared to placebo improve pancreatic beta-cell function. However, moderate exercise resulted in a greater increase in pancreatic beta-cell function compared to metformin intervention. The participants from this trial need to be followed up for a longer period to assess the long-term effects of these interventions.