The inadequate management of agro-waste in intensive agriculture has a severe negative impact on the environment. The valorization of crop residue as a source of crop nutrients is a valid alternative to close the nutrient cycle and reduce the use of external input. In this study, plant material was incorporated into the soil as fresh crop residue, after either composting and vermicomposting processes, to evaluate their effects on tomato yield and nutritional status (petiole sap analysis: NO3 and K+ concentration) over three crop cycles. A control treatment with mineral fertigation and an organic control treatment with goat manure were also included. Enzymatic activity and microbial population in the soil were evaluated. Although no differences between treatments were observed in the first cycle, in the second and third cycles, the yield obtained with the application of organic amendments derived from agro-waste was comparable to the yield obtained with mineral fertilizers. Overall, the sap analysis did not reveal a clear relationship with yield performances. The compost treatment resulted in higher microorganism presence in the soil. Soil dehydrogenase activity (DHA), acid phosphatase activity (ACP), and β-glucosidase activity (β-GLU) were generally more stimulated when organic amendments were used. The study confirms the applicability of soil fertilizers derived from agro-waste as a good alternative to mineral fertilizers.