A 2-year experiment was carried out outdoor on 1-year-old nectarine trees (Big Top grafted on Adesoto 101 Puebla (P. insititia) grown in large (˜0.5 m3) pots filled with a sandy and poorly fertile soil in which, with 4 replicates, the following soil-applied amendment strategies were compared: a) unamended control; b) biochar (16.4 g kg−1 (d.w.)); c) compost (40.0 g kg−1 (d.w.)) and d) biochar mixed with compost, at the same rates of the previous two strategies. Only the first two strategies received mineral fertilizers. We monitored root growth dynamic and assessed tree growth, nutritional status, leaf photosynthetic rate, yield, fruit quality, tree architecture and tree biomass partitioning. Our findings demonstrate that benefits on soil properties and tree growth were mainly attributable to the addition of compost and, to a less extent, by biochar alone (mostly without significant effects), indicating that perennial agro-ecosystems may not immediately respond to biochar application. Strategies influenced root physiology rather than morphology or biomass, as a possible adaptation to the changed growing conditions. However, root growth pattern did not reflect the aboveground tree performance. Compost extended root lifespan and increased photosynthetic leaf efficiency, while biochar reduced root survivorship and increased root turnover, signifying that amendment strategies modify C fixation and alter C budget partitioning within tree organs. The PCA analysis suggests that biochar-induced benefits on tree yield could presumably occur over time. Tree physiology and performance were not outperformed by the mixture of the two amendments, likely because compost hindered potential synergism with biochar. While we conclude that the contemporaneous addition of biochar and compost may not always reflect additive responses on plant performance, we speculate that these matrices can be conveniently combined in the sustainable management of nectarine trees with the aim to replace mineral inputs, preserve soil fertility and fight climate changes.