Crop diversification has been identified as a tool to improve both productive and environmental performances of organic horticulture. We tested the introduction of faba beans in a tomato cropping system—both as preceding crop and in strip cropping (SC)—under different fertilization strategies—faba residues, animal manure, and vegetable compost. We studied: (i) the tomato nutrient uptake and yield and quality; (ii) the soil-N and P, the N-budget, and the mycorrhizal colonization. SC did not provide consistent positive effects on tomato production and quality, namely the N-uptake, N in the tomato yield, the mean fruit weight, and the sugar accumulation in berries, regardless of the type of fertilizers applied. SC improved the tomato dry yield and P-uptake, especially in years when the faba growth and the subsequent yield were problematic. Faba residues could provide sufficient N to sustain tomato production but care should be given in balancing additional N-inputs. Organic fertilization increased the soil-N concentration but did not always translate into an increased yield and a higher quality production, with the risk of escalating N-losses. SC improved the soil-P availability and mycorrhizal colonization in tomato, due to the rhizobia–mycorrhiza-mycorrhiza association, especially when coupled with organic fertilization. Finally, introducing faba as SC holds potential to improve the productive and environmental performance of organic tomato production.