This study evaluated the economic efficiency of seven crop nutrition treatments in relation to soil biological, chemical and physical parameters in a Mediterranean climate. Field experiments were conducted from 2014 to 2016 at two sites in south-western Australia – Wagin and Kojonup, with contrasting rainfall and sandy soil profiles. Treatments included high-input conventional fertilizer, a halved fertiliser rate, biological based amendments, a combination of biological and conventional fertilizers and control. A non-oriented slack based data envelopment analysis (DEA) was used to assess the treatment efficiency based on input use, cost incurred, changes in soil parameters, yield and gross margin. While the high input fertilizer treatments produced the highest yields, the highest gross margins were achieved under the halved fertilizer rate and control at both sites, highlighting the decoupling of yield maximization and economic efficiency. DEA analysis showed that none of the treatment reached full efficiency, with Wagin exhibiting higher overall efficiency scores than Kojonup. Treatment efficiency varied across both sites, where halved fertilizer rate and compost extracts with micronutrients performed best at Kojonup, while liquid nutrient solution, high input conventional and combination of biological and mineral fertilizer were more efficient at Wagin. DEA slack analysis of biological parameters showed consistent decline over two years of cereal cropping. At Wagin, transition from cereal to canola resulted in increased slack values, reflecting shifts in soil biological functioning. Detailed analysis of nitrogen fixing gene nifD slack indicated site specific differences in response. At Kojonup, nifD expression was mainly deficient, which was correlated with soil bulk density, organic carbon and phosphorus. At Wagin, nifD expression was mainly in excess and was also correlated to soil bulk density, phosphorus, organic carbon and aggregation. This study demonstrates the potential of optimizing soil health parameters under different management systems to improve the economic efficiency of crop production.