As a tree management tool, three treatments of crown pruning (total-pruning, half-pruning and no-pruning) were applied to Vitellaria paradoxa (karité) and Parkia biglobosa (néré) in agroforestry parkland systems in Burkina Faso. The area under each tree was divided into four concentric tree influence zones (Zones A: up to 2 m from the tree trunk, B: up to half of the radius of the tree crown, C: up to the edge of the tree crown and D: up to 2 m away from the edge of the tree crown). Millet production under these zones and outside was assessed during two cropping seasons over the study period of three years and the results showed that tree crown pruning had significant effect on millet production and the highest millet grain yield and total dry matter were produced under total-pruned trees (507 ± 49 and 2033 ± 236 kg ha−1 year−1, respectively). Light transmission, transpiration and soil nutrient status under the trees were also analysed in relation to millet production. The results of the analysis showed that total-pruned trees gave the highest millet production due to the reduction by crown pruning of the effects of large tree crowns on PAR transmission below crowns and rates of transpiration by trees. Soil was more fertile closer to the tree trunks than outside tree crowns. This may also be one of the reasons why millet overall performed better under Zone B than outside tree crowns. The higher production of millet under Zone B than under Zone A, the zone closer to the tree trunk, may be due to lower light intensity and more intense competition for water between trees and crops under Zone A. It was concluded that at least in the short term millet production could be improved by crown pruning of both karité and néré, but long term effects may depend on the ability of the trees to maintain the amelioration of soil fertility and on how quickly the trees recover from pruning.