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Background: It is widely accepted that crop yields will be affected by climate change. However, the role played by climate in affecting crop yields vis-a-vis non-climatic stresses, is often unclear, limiting decision choices around efforts to promote increased production in light of multiple stresses.\ud \ud \ud \ud Results: This study quantifies the role of climatic and non-climatic factors affecting multiple crop yields in Uganda, utilizing a systematic approach which involves the use of a two-stage multiple linear regression to identify and characterize the most important drivers of crop yield, examine the location of the key drivers, identify the socio-economic implications of the drivers and identify policy options to enhance agricultural production. We find that non-climatic drivers of crop yields such as forest area dynamics (p = 0.012), wood fuel (p = 0.032) and usage of tractors (0.041) are more important determinants of crop yields than climatic drivers such as precipitation, temperature and CO2 emissions from forest clearance. Climatic drivers are found to multiply existing risks facing production, the significance of which is determined by variability and inadequate distribution of precipitation over the crop growing seasons.\ud \ud \ud \ud Conclusion: The significance and validity of these results is observed in an f-statistic of 50 for the final optimized model when compared to the initial model with an f-statistic of 19.3. Research and agricultural policies have to be streamlined to include not only the climatic elements but also the non-climatic drivers of global, regional and national agricultural systems.