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At present, organic fertilizers are not widely used in intensive arable agriculture, and not much is known about their effects on crop nutrition. In a field experiment at Rothamsted, UK, anaerobic digestate (AD), compost, farmyard manure (FYM), straw, and mixes of amendment + straw, were applied at: 1, 1.75, 2.5 or 3.5 t carbon ha^−1, with all plots receiving the same input of mineral fertilizer. After five seasons of application, plots receiving non-straw amendments had greater straw and grain yield of 28% and 18% respectively, and plots receiving the highest amendment rate had a 37% higher straw and 23% higher grain yield, compared to control plots. Whereas, the straw-only amendment did not increase yield compared to the control. The concentrations of secondary and micro nutrients in the crop, particularly P, Ca, and S in the straw, and P and Fe in the grain, were significantly greater in the crop receiving non-straw amendment compared to the control. Interestingly K, Fe, and Zn were greater in the crop straw treated with the straw-only amendment. Therefore ‘biomass dilution’ of secondary and micro nutrients did not occur in the higher-yielding amended plots after five seasons, and organic fertilizers would improve the quality of high-yielding, intensively produced crops. The study also demonstrates that portable x-ray fluorescence (pXRF) could be a reliable, cost-effective tool for screening potential organic fertilizers.