Accurate, timely, and non-destructive early crop yield prediction at the field scale is essential in addressing changing crop production challenges and mitigating impacts of climate variability. Unmanned aerial vehicles (UAVs) are increasingly popular in recent years for agricultural remote sensing applications such as crop yield forecasting and precision agriculture (PA). The objective of this study was to evaluate the performance of a low-cost UAV-based remote sensing technology for Bambara groundnut yield prediction. A multirotor UAV equipped with a near-infrared sensitive consumer-grade digital camera was used to collect image data during the 2018 growing season (April to August). Flight missions were carried out six times during critical phenological stages of the life-cycle of the monitored crop. Yield was recorded at harvest. Four vegetation indices (VIs) namely normalized difference vegetation index (NDVI), enhanced vegetation index 2 (EVI2), green normalized difference vegetation index (GNDVI), and simple ratio (SR) generated from the Red-Green-Near Infrared bands were calculated using the georeferenced orthomosaic UAV images. Pearson’s product-moment correlation coefficient (r) and Bland–Altman testing showed a significant agreement between remotely and proximally sensed VIs. Significant and positive correlations were found between the four VIs and yield, with the strongest relationship observed between SR and yield at podfilling stage (r = 0.81, P < 0.01). Multi-temporal accumulative VIs improved yield prediction significantly with the best index being ∑SR and the best interval being from podfilling to maturity (r = 0.88, P < 0.01). The accumulated ∑SR from podfilling to maturity resulted in higher prediction accuracy with a coefficient of determination (R 2) of 0.71, root mean square error (RMSE) of 0.20 and mean absolute percentage error (MAPE) of 14.2% than SR spectral index at a single stage (R 2 = 0.68, RMSE = 0.24, MAPE = 15.1%). Finally, a yield map was generated using the model developed, to better understand the within-field spatial variations of yield for future site-specific or variable-rate application operations.