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The effects of organic (manure, cover crop) and mineral fertilisers on total yield, soil phosphorus (P) and potassium (K) dynamics and soil pH changes were studied over 10 years. Five field crops (spring barley, red clover, winter wheat, field pea, potato) were grown organically and conventionally in rotation. The total yield of the five crops fertilized similarly was 24–25% higher in conventionally fertilised treatments than in organic treatments. The higher yielding conventionally fertilised treatments (annual total yield 29.0–29.8 t ha–1) removed 12–18 kg ha–1 P and 45–73 kg ha–1 K per year, which was respectively 28–35% and 28–40% higher than organic treatments. The soil became more acidic in the conventional system (pH 5.4–5.9 versus 5.9–6.3). The highest annual P and K uptake was by potato, followed by winter wheat. Use of winter cover crops and composted cattle manure in the organic system did not maintain the levels of P and K in the soil at baseline.