Background: The use of compost may relieve the factors that limit productivity in intensive agricultural systems, such as soil organic matter depletion and soil sickness. Concomitantly, the practice of on-farm composting allows the recycle of cropping green residues into new productive processes. Results: We produced four vegetable composts by using tomato biomass residues in an on-farm composting plant. The tomato-based composts were assessed for their chemical, microbiological properties, and their effects on soils and plants were evaluated after their application within a tomato cropping system. Compost characteristics affected plant development and productivity through increased nutrient uptake and biostimulation functions. Soil biological activities, including basal respiration, fluorescein diacetate hydrolysis, β-glucosidase, dehydrogenase, alkaline phosphatase, arylsulphatase, and Biolog community levels of physiological profiles, were differently affected by the on-farm tomato-based composts.