Despite the prevalent application of biochar and organic manure in agro-ecosystems, their combined effects on the restoration of sandy soils mediated by microbial mechanisms remain understudied. Here, we conducted a field experiment in the Mu Us sandy land to characterize the responses of soil microbiomes (bacteria, fungi, protists) and ecosystem functions (soil fertility, plant growth, material cycling, carbon mineralization potential) to co-application of biochar and organic manure with planting. The experiment incorporated three levels of biochar (0, 25, 50 t/hm2), two levels of organic manure (0, 10 t/hm2), and four levels of plants (1, 3, 5, 9 legume or grass species). The results indicated that both biochar and organic manure, but not plants, contributed to significant enhancement in soil multifunctionality. The greatest soil multifunctionality was observed at the high biochar rate with organic manure, which increased by 52 % compared to the lowest multifunctionality observed under no application of biochar and organic manure. This was manifested by increased contents of soil organic carbon (761 %), total nitrogen (207 %), and total phosphorus (67 %), alongside stimulated plant growth, despite greater carbon mineralization potential. Various microbial communities exhibited differential responses to biochar and organic manure treatments, with decrease in bacterial diversity and increase in protistan diversity. Fungal diversity positively responded to biochar application rate only. Soil organic carbon, total nitrogen, and total phosphorus emerged as the primary factors driving shifts in bacterial, fungal, and protistan communities. The complexity of microbial networks varied across treatments and positively correlated with the rate of organic manure (bacteria), biochar (fungi), or both (protist), but there was no response to planting. Linear regression analysis revealed a negative correlation between bacterial diversity and soil multifunctionality (R2 = 0.14, p G 0.01). Protistan diversity (R2 = 0.14, p G 0.01) and microbial network complexity (bacteria: R2 = 0.25, p G 0.001; fungi: R2 = 0.13, p G 0.01; protists: R2 = 0.36, p G 0.001) were positively correlated with soil multifunctionality. Variance partitioning analysis indicated that microbial network complexity had a greater influence on soil multifunctionality than community diversity, underscoring the role of microbial interactions. Our results indicate that the co-application of biochar and organic manure, not plants, enhances the multi-functionality of sandy loam soil, with microbiome complexity serving as a critical predictor of changes in soil functions.