Abstract: Different pruning methods were applied on Capsicum annuum L.var.grossum grown on an organic substrate to observe their effects on the morphology, photochemical activity and yield of the plants. The results showed that the photosynthetic performance indices, PI_ABS and PI_CSm, and the driving forces, DF_ABS and DF_CSm, were significantly greater when the 3-stem-pruningwas applied. The pruning also rendered the highest leaf PSⅡ photochemical activity among all treatments.Pruning, in general, significantly affected the plant growth. The 2-stem-pruning resulted in significantly greatest plant height, stem diameter and internode length, while the 3-stem-pruning yielded the highest root/shoot ratio. Pruning also affected the fruit count per plant and single fruit weight.The 4-stem-pruning produced the highest fruit count but lowest on single fruit weight, as the 3-stem-pruning delivereda significantly higher yield (up to 2.017 kg per plant) than the other pruning methods. In addition, the 3-stem-pruning significantly increased the soluble sugar content and sugar/acid ratio inthe fruits.