Earlier research largely ignored the effects of climate change on the growth of agricultural total factor productivity (TFP) in Africa. This study shows how climate inputs impact TFP growth in addition to other productivity growth indicators and metrics, as well as how they can impact overall input efficiency as productivity drivers. We use a panel of 42 African nations from 1999 to 2019 and a nonparametric data envelopment analysis-Malmquist technique. The non-parametric analysis revealed that the average growth rate of the non-climate-induced TFP estimates was 1.9%, while the average growth rate of the climate-induced TFP estimates was 2.4%. Accounting for temperature and precipitation separately, TFP grew by 2.3% on average. This growth rate (2.3%) is slightly less than the combined effect of temperature and precipitation (2.4%) but higher than the typical TFP growth rate (1.9%) that ignores climate variables, indicating that TFP growth in African agriculture risks being underestimated when climate inputs are ignored. We also find the distribution of the climate effects to vary across regions. In northern Africa, for example, the temperature-induced TFP growth rates were negative due to rising temperature in the region. Evidence from the decomposed TFP estimates indicates that climate variables also influence productivity determinants. However, technology improvement is fundamental to mitigating the effects of extreme weather inputs on TFP growth in Africa's agriculture. As a result, a few policy suggestions are provided to help policymakers deal with the effects of climate change on TFP growth in Africa's agriculture and ensure food security. The study advocated for a reevaluation of the climate–agriculture effect in order to fully comprehend the role of climate factors and their contributions to agricultural TFP growth in Africa.