Coffee farming is crucial for Brazil, the world leader in coffee production and exportation. Strategies like the “safra zero”, which involve practices such as skeleton pruning, have been adopted to rejuvenate coffee plants and optimize production in alternate years. This contributes to reducing costs and labor demand. Faced with the environmental and economic challenges of coffee cultivation, bio-inputs stand out as a sustainable alternative in crop management, especially during vegetative recovery phases. Therefore, this study was developed to evaluate the effects of applying bio-inputs to coffee plants subjected to skeleton pruning. The experiment was carried out using a randomized block design, in split plots, with eight treatments: five bacterial strains (UNIFENAS 100-94, Azospirillum brasilense, Pseudomonas fluorescens, Bacillus megaterium, and B. subtilis), organized into six combinations, plus a treatment with A. brasilense and a control, with four replicates. Applications occurred in March, April, August, and September. Plant height, plagiotropic branch length, and the number of buds were evaluated every 30 days. At the end, soil and leaf chemical analyses were also performed. Mix 2 (UNIFENAS 100-94 + P. fluorescens) reached the best performance, with increases in plant height, plagiotropic branch length, and number of buds. All analyzed variables evolved over time. Nutrient levels increased with the use of bio-inputs. It is concluded that these inputs have potential in the post-pruning management of coffee plants.