The impact of elevated CO2 (eCO2) on grain nutrient concentration is becoming a global concern in terms of future human nutrition. Previous research has shown that eCO2 can alter the availability and uptake of nutrients in crops. However, the interactive effects of long-term eCO2 and soil types on the concentrations of nutrients in grain are poorly understood. By understanding such effects, we are able to develop management practices that maintain grain nutritional quality while improving crop yield in response to future climatic conditions. We conducted a seven-year experiment of free air CO2 enrichment (FACE) with a rotation of wheat, field pea and canola grown in a Chromosol (Luvisol), Vertosol (Vertisol) and Calcarosol (Calcic Xerosol) under ambient CO2 (aCO2) (390 ± 10 μmol mol-1) or eCO2 (550 ± 30 μmol mol-1). The concentration and amount of five macro- and four micro-nutrients in grain over the seven years were determined. Compared to aCO2, the concentrations of N, P and Zn decreased by 6%, 5% and 10% under eCO2, respectively, irrespective of soil, crop and year. A greater decrease in N concentration was found in canola and wheat compared to field pea. The reduction in P and Mg concentration of canola was significant in Chromosol, but not in the Vertosol nor Calcarosol soils. The concentrations of K, Fe, Mn and Cu were not affected by eCO2 in any crop grown in the soils tested. Furthermore, eCO2 significantly decreased soil labile N and P and exchangeable Mg and Cu due to greater nutrient uptake, which was in part ascribed to the decreased nutrient accumulation in crop grains. It appears that eCO2 lowers the nutritional quality (nutrient concentration) in grains of non-legume crops, and that the extent of this decrease was greater in relatively fertile than infertile soils.