Pruning and nutrient supply after pruning are crucial to restore growth and productivity of old, unproductive coffee trees. The effect of pruning type (stumping, heavy pruning and light pruning) and fertilizer rate (100, 140, 180 and 220 g nitrogen, phosphorus and sulphur (NPS) mixed fertilizer per tree per year) on coffee yield and yield components and fertilizer agronomic efficiency (AE) was studied in southwest Ethiopia to identify the best pruning type and fertilizer rate combination for high crop productivity and AE. The experiment was conducted in a split-plot design with three replicates, where pruning type was the whole-plot factor and fertilizer rate was the subplot factor. Both main and interaction effects of pruning type and fertilizer rate on response variables were significant. Stumping and heavy pruning showed a much higher number of primary branches and fruiting nodes per tree than did light pruning. The 100 g fertilizer rate showed a significantly higher number of verticals and fruiting nodes per tree, yield and AE than did the other rates. Besides, the combination of heavy pruning and 100 g, stumping and 220 g, and stumping and 100 g provided a much higher number of fruiting nodes per tree, yield and AE; number of fruiting nodes per tree, canopy diameter and yield; and yield and AE, respectively than others. These findings show the importance of stumping and heavy pruning each combined with 100 g NPS fertilizer for renewing coffee productivity and maximizing AE in the study area.