Harnessing the rhizosphere microbiome to engineer resilient agricultural systems is pivotal for ensuring global food security under accelerating climate change. Achieving this goal, however, demands a unified framework to disentangle the multi-layered drivers of microbial community assembly. Here, we synthesize recent advances into a hierarchical conceptual framework. We delineate how foundational soil physicochemical properties establish a baseline environmental filter. Upon this foundation, the host genotype exerts powerful endogenous control, actively shaping microbial communities through its root architecture, exudate chemistry, and rhizosphere redox dynamics. This co-evolved equilibrium is subsequently modulated by exogenous forces, notably agricultural management practices and climatic perturbations. Moving beyond isolated-factor approaches, we highlight their synergistic interactions as a central yet underexplored frontier. Building on this integrated understanding, we evaluate emerging strategies for microbiome engineering, from soil and host-targeted approaches to the design of sustainable agronomic practices. Finally, we propose future research directions that leverage multi-omics and synthetic communities to shift from descriptive ecology toward predictive design, thereby advancing a sustainable agricultural future. This review synthesizes a novel framework for understanding the assembly and regulation of rhizosphere microbiomes, facilitating their integration into sustainable agroecosystems.