Improved farming practices are needed to produce more food in a sustainable way. This study assessed 12 combinations of cover crop mixtures and amendment treatments and their effects on shoot and root dry (matter (DM) weights, nitrogen (N), phosphorus (P) and potassium (K) uptakes in plants, Mehlich-3 extractable P (PM3) and K (KM3). Shoot and root DM weights were increased by 30–63% with combinations of clover-based cover crop mixtures and 65 Mg ha−1 of municipal solid food waste (MSFW) compared with synthetic fertilizer. The combination of clover-based cover crop mixtures with MSFW increased N uptake by 38 and 30%, P uptake by 57 and 40% and K uptake by 77 and 77% compared with fertilized and unfertilized treatments, respectively. The combination of vetch-based cover crop mixtures with MSFW had no effect on N uptake, but increased P uptake on average by 43%, and K uptake on average by 11% compared with fertilized and unfertilized treatments. The highest soil PM3 and KM3 values were obtained with additions of MSFW, while the lowest were obtained with synthetic fertilizer indicating that the amount of P and K added with MSFW were greater than cover crop needs. Combining cover crop mixtures and MSFW at levels recommended for N fertilization allows meeting cover crops’ nutrient needs and increases biomass inputs to agricultural soils, but long-term monitoring of soil P is required to limit potential P build-up.