Current farming systems are highly reliant on chemical fertilizers (CF), which negatively affect soil health, the environment, and crop productivity. Substituting organic fertilizer for chemical fertilizer (CF) is an important agricultural practice that improves soil health and crop productivity and is eco-friendly. To explore the effects of organic fertilizer in the form of cattle manure (CM) or poultry manure (PM) combined with CF on soil properties, leaf physiological traits, and grain physiochemical characteristics of rice, a 2-year field experiment was conducted in a dual cropping system with six treatments: Neg-CF (no N fertilizer control), Pos-CF (100% CF), High-CM (60% CM + 40% CF), Low-CM (30% CM + 70% CF), High-PM (60% PM + 40% CF), and Low-PM (30% PM + 70% CF). The results exhibited that the adding of organic manure significantly improved soil chemical traits such as soil organic C (SOC), total N (TN), and available N (AN). Similarly, applying the combined fertilizer led to significant increases in the leaf net photosynthetic rate (Pn), SPAD values, and rice grain nutritional and cooking characteristics according to Rapid Visco-Analyzer (RVA) profile. Average increases in SOC, TN, Pn, starch content (SC), and amylose content (AC) were 16%, 12%, 9%, 7%, 9%, and 12%, respectively, across the year in the Low-PM compared to the Pos-CF treatment. Moreover, the manure amendments significantly altered the RVA profile attributes, including peak viscosity, tough viscosity, final viscosity, and the setback and pasting temperatures compared to Pos-CF. Linear regression analysis revealed that SOC and TN were positively associated with leaf Pn and SPAD values. Further, leaf Pn and SPAD were positively correlated with rice grain SC and AC. The correlation heat map analyses revealed a positive correlation in the RVA profile between the soil properties and leaf physiological traits. These correlation analyses showed that the increase in soil chemical traits and leaf physiological activities played a significant role in higher rice grain nutritional and cooking quality. Overall, the findings of this study show that the integrated use of organic fertilizers and CF in rice fields enhances soil functionality and the quality of rice on a sustainable basis.