This study tested the hypothesis that integrating biochar with organic manure and recommended inorganic fertilisers can simultaneously enhance rice grain quality, nutrient use efficiency and economic sustainability compared with chemical fertilisers. The urgency of confirming this hypothesis stems from rising fertiliser costs, declining soil fertility, widespread micronutrient deficiencies and the need to sustain rice productivity and quality under changing climate conditions. Synthesising results across two seasons (2023–2024), we found that the integrated approach markedly improved grain quality and nutrient dynamics, with the best performing combination recording protein content of 10.64 % and 11.14 % starch content, of 70.78 % and 71.69 % hulling recovery of 83.64 % and 84.53 % and milling recovery of 73.56 % and 74.21 %, respectively. These improvements were accompanied by the highest nitrogen (N), phosphorus (P), potassium (K) and zinc (Zn) content and uptake in both grain and straw, demonstrating enhanced nutrient assimilation and translocation rather than isolated fertiliser effects. The breakthrough of this work lies in establishing a previously underexplored interdisciplinary linkage among soil carbon amendments, micronutrient nutrition, grain quality and processing efficiency, thereby connecting soil health management with food quality and agribusiness outcomes. Integrated application of biochar, farmyard manure and inorganic fertilisers resulted in a significant improvement in rice productivity, a 12–18 % yield increase over sole chemical fertilisation, along with enhanced grain quality and nutrient uptake. Future research should focus on long-term validation across diverse agro-ecological regions, optimisation of biochar sources, carbon footprint and credit assessments with precision nutrient management, while addressing challenges related to biochar availability, standardisation and farmer adoption.