Microbial-based products are essential for sustainable agriculture, yet inconsistent performance and limited mechanistic understanding constrain their adoption. While terminology varies globally—from "bioinputs" to "microbial products"—this linguistic diversity reflects a deeper conceptual gap. Historically, the sector has relied on a successful but empirical Bioinputs 1.0 paradigm, based on phenotypic screening and a "black box" approach to efficacy. We propose Bioinputs 2.0 as an evolutionary framework grounded in genomics, functional biology, and advanced formulation. This paradigm integrates microbial ecology, metabolite-driven bioactivity, and systems-level interactions, positioning formulation as an integral design component rather than a secondary step. Transitioning from empirical discovery to knowledge-driven design is necessary to ensure reliable, scalable applications. While particularly evident in biocontrol, this shift provides a stronger basis for interpreting field responses in plant growth-promoting microorganisms. Overall, Bioinputs 2.0 emphasizes integrated, context-dependent biological systems to bridge the gap between laboratory insights and consistent field performance.