The economics of coffee plantations is intrinsically linked to pruning, which can improve the canopy architecture and thereby increase productivity. However, recommended pruning times on conilon coffee plantations have been made on an entirely empirical basis. In this study, by evaluating growth, photosynthetic gas exchanges, starch accumulation and crop productivity, the effects of pruning at different times between harvest and flowering were investigated for six conilon coffee clones with distinct stages of fruit maturation (early, intermediate and late). Clones with an early maturation stage were pruned at four different times: 0, 30, 60 and 90 days after harvest (DAH). Intermediate clones were pruned at 0, 30 and 60 DAH, and late clones were pruned at 0 and 30 DAH. Overall, the rates of shoot growth and net photosynthesis, the stomatal conductance and the crop yield were not affected by the pruning treatments in any of the clones. In addition, pruning times did not affect the concentrations of starch or the photochemical efficiency of photosystem II. The carbon isotope composition ratio was marginally affected by the treatments. These results suggest that the pruning time after harvests is relatively unimportant and pruning operations can be scheduled to optimise the use of labour, which directly impacts the production costs of coffee.