<p>Direct-seeded rice (DSR) offers benefits in terms of water and labor savings, but its success depends on the establishment method and nutrient management. A two-year field study was conducted in a split plot design with two main plots (puddled DSR and dry DSR) and seven sub-plot treatments (recommended dose of fertilizer (RDF), soil test based fertilization (STBF) and five combinations of 75% STBF with poultry manure or vermicompost along with NPK microbial consortia) to assess the effects of establishment method and various nutrient management on yield, nutrient dynamics, soil enzymatic activity, microbial populations, and nutrient stoichiometry in rice. Results indicate that puddled DSR recorded significantly higher grain (4632.14&#xa0;kg ha^− 1) and straw yield (6889.02&#xa0;kg ha^− 1), with increased nitrogen, phosphorus and potassium uptake in grain and straw. In contrast, dry DSR displayed significantly higher soil microbial biomass carbon (147.26&#xa0;mg kg^− 1 soil), bacterial and fungal populations. Under nutrient management, application of 75% STBF + vermicompost + NPK consortia consistently outperformed sole inorganic fertilization (RDF and STBF), thereby enhancing the seed and straw yield (4755.25 and 7145.75&#xa0;kg ha^− 1, respectively), nutrient uptake, and dehydrogenase activity (79.48&#xa0;µg TPF g^− 1 soil hr^− 1). Grain nutrient stoichiometry (NP, PK, NK ratios) was more balanced under puddled DSR and integrated nutrient managements. These findings demonstrate that the establishment method and nutrient management influenced crop productivity, soil biological functioning, and nutrient balance in DSR systems, with integrated approaches offering a pathway to sustain both yield and soil health.</p>