The aim of this work was to compare the application of biochar, compost, and their mixtures on soil fertility and crop yields using a volcanic Mediterranean soil. For this reason, three types of organic amendments (OAs) were selected: compost1, made from olive mill waste and orchard pruning residues; compost2, made from olive mill waste, animal manure and wool residues; and biochar made from beech wood pyrolyzed at 550 °C. When selected, the OAs were characterized chemically for organic carbon (OC), total N, pH, electric conductivity (EC) and the bulk fraction of organic matter using ¹³C CPMAS NMR spectroscopy. In addition, soil chemistry was analysed at the end of each year for the following parameters: pH, OC, total N, CaCO₃, P₂O₅, NH₄, FDA and EC. Results showed that biochar had the highest OC and the lowest N and EC compared to both composts. Moreover, ¹³C CPMAS NMR showed that biochar had the lowest content of O-alkyl, methoxyl- and alkyl-C and the highest content of aromatic-C. On the other hand, compost2 and compost2+biochar mixture reduced Aubergine yield by −60% and −40%, respectively, and tomato yield by −50% and −100%, respectively. Nevertheless, a significant increase in onion and rape yields were observed when compost1, compost1+biochar and compost2 were applied, while biochar and compost2+biochar significantly decreased the yield of these crops. Overall, our results highlight that the effect of OAs on crops yield is largely variable and influenced by the interaction with soil chemistry.