Enhancing soil multifunctionality is fundamental to achieving sustainable agricultural production in semi-arid regions. This study investigated the interactive effects of cropping systems and fertilization regimes on soil multifunctionality, with particular emphasis on the underlying microbial mechanisms. A field experiment employing a split-plot design was conducted on the Loess Plateau, including two cropping systems (continuous foxtail millet, CM; foxtail millet-mung bean rotation, RM) and four fertilization treatments (no fertilizer, CK; chemical nitrogen and phosphorus fertilizer, NP; organic fertilizer, OF; combined organic-inorganic fertilization, NPO). Soil physicochemical properties, enzyme activities, and microbial community characteristics were analyzed. The results demonstrated that the combination of crop rotation with integrated organic-inorganic fertilization (RMNPO) most effectively enhanced soil multifunctionality. Microbial community analyses revealed distinct regulatory patterns: cropping systems primarily reshaped bacterial community composition, whereas fertilization regimes exerted a stronger influence on fungal communities. Notably, fungal taxa, particularly Ascomycota and Basidiomycota, were identified as key biotic drivers. Their community structure strongly predicted multifunctionality, explaining more than 90% of its variation under the NPO treatment. At the genus level, specific fungal taxa (Fusarium, Metarhizium, and Chaetomium) were identified, whose reduced abundance under optimized management practices was closely associated with enhanced multifunctionality. Random forest modeling further indicated that fungal genera possessed greater predictive capacity for multifunctionality than bacterial genera. Moreover, the stability of fungal co-occurrence networks showed a significant positive correlation with multifunctionality. Integrative analysis using partial least squares structural equation modeling (PLS-SEM) elucidated distinct functional pathways: fertilization regimes influenced multifunctionality primarily through direct effects on bacterial community structure, whereas cropping systems exerted stronger indirect effects by shaping fungal communities, which ultimately governed multifunctionality outcomes. Collectively, these findings indicate that sustainable soil management strategies should extend beyond enhancing microbial diversity to fostering functionally relevant microbial assemblages and stabilizing their interaction networks.