The effect of shoot pruning (2, 3 and 4 branches per plant) and fruit position selection (on main branch vs on main and lateral branches) on yield and qualitative characteristics of two greenhouse grown pepper (Capsicum annuum L.) cultivars (Torkal and Paramo) was studied through a factorial experiment arranged in a Completely Randomized Block Design, of three replications. Results indicated that the Red cultivar bore a higher fruit number (14.43), total yield (2263.43 grams per plant) and marketable yield (2205.71 gram per plant), second grade fruits (736.86 gram per plant), total soluble solids, vitamin C as well as total leaf chlorophyll in comparison with the Orange cultivar. Through increase in the shoot number, yield characteristics (except fruit weight) increased in a way that four stem plants carried the highest yield traits. By increasing the shoot number per plant, it’s height and node number decreased. Two stem plants revealed the highest qualitative characteristics as regards vitamin C of the fruit, total leaf chlorophyll and fruit carotenoid. Selecting fruits on main and lateral branches resulted in a more fruit number (14.32 fruits per plant), total yield (2190.12 gram per plant), number of second grade fruit (659.49 gram per plant) in comparison with a selection of fruits on main branches. By selection of fruits on the main branch, bigger size fruits (fruit weight of 161.78 gram per plant) were obtained. Concerning the interaction effects, Red cultivar displayed more pronounced changes than the Orange one in the case of fruit being selected on main and lateral branches. There wasn’t any difference observed in fruit on different position when pepper plant was pruned for four stems to remain. With plant pruned on three stem basis and with fruit on main and lateral branches, greater yield was the result. Finally because of higher yields and observance of no negative effects on fruit quality, an arrangement of four stem plant and a selection of fruits on the main branches is finally recommended.