Background and aims <p>Applying organic amendments is an efficient agronomic practice for increasing crop productivity in saline–alkali farmlands. However, it remains unclear whether and how microbiota assist crops in nutrient uptake under the application of organic amendments.</p> Methods <p>A field experiment was conducted to investigate the impact of organic amendments on sunflower nutrient uptake and the underlying microbial mechanisms in a saline–alkali farmland. We considered three fertilization treatments, without organic amendment (CK), lignite-based organic amendment of 4.5 t ha⁻¹ (LBF), and sheep manure fertilizer of 5 t ha⁻¹ (SMF).</p> Results <p>In relation to the CK, the LBF and SMF increased sunflower nitrogen and phosphorus uptake, as well as yield, with the LBF performing better than the SMF. After applying the LBF and SMF, the sunflower rhizosphere enriched nine and six stable beneficial microbes, respectively, such as, <i>Pseudomonas</i>, <i>MND1</i>, <i>Penicillium</i>, and <i>Mortierella</i>, over more than two years. The LBF and SMF improved rhizosphere growth-promoting functions, including nitrogen fixation, organic phosphorus mineralization, and inorganic phosphorus solubilization, in relation to the CK. The stable beneficial microbes were positively associated with multiple nitrogen and phosphorus metabolic processes, indicating their potential role in facilitating sunflower nitrogen and phosphorus uptake. Moreover, these microbes may play a pivotal role in enhancing the stability of the microbial co-occurrence network, which could be positively related to sunflower nitrogen and phosphorus uptake.</p> Conclusion <p>The application of organic amendments could promote crop nutrient uptake by assisting crops in recruiting stable beneficial soil microbes, which may facilitate nitrogen and phosphorus transformations and enhance microbial community stability in a saline–alkali farmland.</p>