East African highland bananas and climbing beans are important crops for food and income in the highlands of Uganda. Intercropping of banana with legume crops is a common practice, yet climbing bean intercropping with perennials has rarely been studied in Uganda. To understand how best to improve the production system, we assessed the effects of pruning of banana leaves on light availability for climbing beans, resulting effects on bean yields and potential differences in shade tolerance between two climbing bean varieties in the eastern and southwestern highlands of Uganda. Measurements of the transmission of photosynthetically active radiation (PAR) through the banana canopy were combined with yield measurements of a local and improved climbing bean variety and with banana pseudostem girth in two seasons (2016A and 2016B). We also compared yields of intercropped with sole-cropped climbing beans. The mean fractions of PAR transmitted through the banana canopy-hence available for beans-were 0.43 on pruned and 0.38 on non-pruned subplots, a significant 15% difference. The improved light availability did not increase climbing bean yield. Although no direct relationship between light interception and bean yields was found, bean yields on the most and least shaded parts of the intercropped fields differed significantly, suggesting that beans do benefit from improved light availability in intercropping. Generally, yields of sole-cropped beans were significantly larger than of intercropped beans, but we could not single out the effects of competition for light, water, and/or nutrients. The bean varieties responded similarly to the pruning treatments. The local variety tended to perform relatively better in intercropping, the improved variety in sole cropping, though differences were not significant overall. Pruning and retention of eight banana leaves over the course of a season did not affect banana pseudostem girths in the mature banana plantations. Although light availability improved, farmers may not expect a major effect on bean yield. Future research may focus on the effects of a lower number of leaves retained, comparing a number of bean varieties for suitability in sole or intercropping, or on other factors influencing the relation between the two crops such as relative plant densities of beans and bananas.