<p><b>Purpose</b>: This study aimed to evaluate the remediation effects of combining acid-modified biochar with soybean meal—a waste-derived organic amendment—on saline-alkali soil, which severely constrains agricultural productivity in regions such as China’s Yellow River Delta. <b>Methods</b>: A pot experiment with wheat (Triticum aestivum) compared treatments of low- and high-dose acid-modified biochar, soybean meal, and their combinations, assessing rhizosphere soil properties, microbiome composition and potential functions, key enzyme activities, and plant physiological traits. <b>Results</b>: The combined application significantly reduced soil pH and increased total nitrogen and total carbon by 24.6% and 16.0%, respectively. When applied alone, both amendments elevated bacterial gene abundance and sucrase activity, whereas only acid-modified biochar increased fungal gene abundance and only soybean meal enhanced urease activity. Phospholipid fatty acid profiling and high-throughput sequencing revealed that both amendments significantly shifted soil microbial community structure and promoted key microbial groups such as Actinomycetes and nitrogen-fixing bacteria. Ultimately, both acid-modified biochar and soybean meal improved wheat growth and stress resistance, with their combination producing the strongest effect. <b>Conclusion</b>: These findings demonstrate that acid-modified biochar and soybean meal act synergistically to alleviate saline-alkali stress by improving rhizosphere properties, increasing microbial biomass, and specifically modulating microbial community abundance and composition, offering a sustainable and scalable strategy for saline-alkali soil reclamation.</p> Graphical Abstract <p></p>