Spinach is rich in minerals, vitamins, phytochemicals and bioactive compounds with health-beneficial effects; however, this plant also tends to accumulate oxalates and nitrates in their leaves. Apart from genotype, nutrition is the pre-harvest factor that mostly affects quality attributes at harvest. Particularly, the application of compost extracts (CE) may induce resistance against soil-borne diseases and favour secondary metabolism, increasing antioxidant capacity. The objective of this study was to evaluate the effects of different types of fertilization with or without the addition of CE, on harvest quality and shelf life of minimally processed spinach (Spinacia oleracea, var. Shrike RZ) stored during 12 days at 4 °C. A compost extract (CE) was prepared by mixing a compost from agri-food wastes (vine pruning, leek waste and olive mill waste) with deionized water. CE foliar applications were done from days 28 and 56 after sowing. The treatments applied were: Control; Control + CE; NPK (inorganic NPK fertilizer 15-15-15); NPK + CE; DMPP (ENTEC Nitrofoska® plus the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP)) and DMPP + CE. After harvest, spinach leaves were minimally processed and packaged to generate a passive modified atmosphere. Nitrate content in the control treatment was reduced by the addition of CE, although in the rest of the treatments, CE addition did not produce any effect. For nitrite contents, the lowest value was obtained for the Control + CE. Moreover, the oxalate content was the lowest for the control treatment with a decreasing trend throughout the storage. The treatment Control + CE also showed the highest initial total phenolic contents, with very similar values at the end of shelf life to those observed at harvest for all the treatments. The highest differences in color as regards the initial values were detected for DMPP. Microbial loads increased for all the treatments without differences between them. The atmosphere reached at the end of the cold storage was the same for all the cases, with CO2 and O2 around 10 kPa for each one of them. After 12 days at 4 °C, all the treatments were above the limit of usability, with the spinach leaves acceptable for consumption. The results found in this study indicate that the addition of CE might be convenient for obtaining spinach rich in bioactive compounds and with low concentrations of antinutritional factors, without affecting the microbial load of the final product.