Organic amendments as partial replacements for synthetic fertilizers in foxtail millet

The rapid expansion of the livestock industry has generated large amounts of manure, posing environmental risks. Composted manure improves soil quality (SQI) and crop yield. However, the effects of different manure types on soil ecological multifunctionality (EMF) and microbial functions in foxtail millet fields remain unclear. A two-year experiment with various manure types was conducted to evaluate soil properties, microbial communities, and their effects on nitrogen use efficiency (NUE) in foxtail millet. At a nitrogen application rate of 225 kg ha− 1, the 50% organic replacement treatments (cow manure, pig manure, and sheep manure) mitigated soil alkalization and improved soil nutrient levels and enzyme activities, resulting in higher SQI and EMF, with the pig manure replacement treatment performing best. Improved soil nutrient levels enhanced microbial community diversity and network stability, strengthened soil carbon and nitrogen cycling, and thus improved soil EMF, which directly promoted NUE and yield in foxtail millet. From 2022 to 2023, partial organic substitution treatments increased soil SQI and crop yield by 2.85–4.73 times and 1.03–1.08 times, respectively, compared to the inorganic fertilizer treatment. Soil physicochemical properties and microbial functions (mainly carbon and nitrogen cycling) were key direct drivers of EMF. Notably, key microbial phyla, such as Proteobacteria, were significantly enriched in partial organic replacement treatments, playing a crucial role in stabilizing microbial network structures and maintaining community functions. Additionally, pH changes were the primary driver influencing soil microbial communities. This study confirmed that partial organic replacement enhanced soil EMF by mitigating soil alkalization, boosting soil nutrient and enzyme levels, and optimizing microbial traits, thereby improving crop NUE and yield. Locally, partial pig manure replacement maximized yield, while partial cow manure replacement optimized grain quality. Our findings provide valuable guidance for scientific fertilization practices and ecological integrity. Organic manure enhances soil microbial diversity and soil ecological multifunctionality (EMF). Soil elements and microbial function contributed positively to EMF. Proteobacteria stabilized microbial networks and enhanced C/N cycling functions. Organic manure application enhanced foxtail millet nitrogen use efficiency by improving soil EMF. Optimal fertilization employed pig manure for maximum yield and cow manure for better grain quality.