Climate change and natural disasters are the main risks to African agricultural production. Given that these factors affect poor countries more, we attempted to identify the economic taxonomy that can adequately describe the most affected African countries and the countries that can cope with these factors. This study explored the impacts of climate change and natural disasters on the total agricultural production in African countries while differentiating these countries by the income level and Least Developed Countries taxonomies. Two country-level panel data were collected covering 55 and 26 years in Africa for this purpose. The findings of this study first highlight that in the long and short terms, temperature is the main climatic factor affecting agricultural production. Second, in the short term, droughts negatively impact African agrarian production regardless of the countries’ development states. Third, the poor countries in these respective taxonomies significantly experienced the negative impacts of climate change and natural disasters. However, the impact of climate factors on agricultural production in middle-income countries and non-least developed countries are less evident. The heterogeneity of the impact of climate change and natural disasters on agriculture across African countries based on their development states. Therefore, the agriculture policy needs to implement as priority in low income or least developed African countries.