Aims <p>Newly reclaimed cultivated soils typically exhibit low fertility and productivity, making quality assessment crucial. Conventional soil quality assessments often overlook the functional traits of microbial communities. This study aimed to investigate the effects of organic amendments on soil quality and microbial functional traits, and develop a novel soil quality assessment index by integrating microbial functional traits and validating its predictive capability in productivity.</p> Methods <p>We investigated the effects of three organic amendments (pig manure, corn straw biochar, and co-application of the former two) on soil properties, microbial communities, and rice yield in a newly reclaimed farmland located in Zhejiang Province, China. Based on these responses, we developed a novel SQI by integrating microbial functional indicators into a conventional framework and evaluated the predictive performance of both indices for rice yield.</p> Results <p>All three fertilizer treatments significantly increased soil organic carbon (SOC), total nitrogen (TN), and sucrase activity (SA). Microbial diversity and C/N/P metabolic potential were also significantly enhanced, which exhibited an active association with rice yield. Notably, the correlation between rice yield and the novel index was significantly stronger (R² = 0.88) than that derived from the traditional parameters (R² = 0.54).</p> Conclusions <p>Organic amendments have improved the quality of newly reclaimed soils. Incorporating microbial functional indicators into soil quality assessment demonstrates significant advantages over traditional evaluation methods in terms of aligning with actual crop yields. This study offers an improved strategy for enhancing the accuracy of soil quality assessment and provides technical support for sustainable soil management.</p>