This study interrogates the viability of a mission-oriented bioeconomy transition, as articulated in India’s BioE3 framework, in delivering integrated Economy–Environment–Employment (E3) outcomes within Bihar, a structurally constrained regional economy. Departing from normative optimism, the analysis situates the bioeconomy within a theoretically synthesized framework that bridges Mission-Oriented Innovation Systems (MOIS) and Sustainable Structural Transformation (SST), while explicitly internalizing ecological and socio-economic risks, including land-use competition, monocultural intensification, and distributional inequities. Methodologically, the study deploys a multi-layered modelling architecture integrating a high-resolution Social Accounting Matrix (SAM), a dynamically updated input–output model, and sector-specific partial equilibrium modules, calibrated using state-level panel data spanning 2010–2023. Model robustness is ensured through extensive sensitivity testing, stochastic simulations, and scenario-based stress analysis. Empirically grounded counterfactuals—Business-as-Usual (BAU), Moderate Bioeconomy Transition (MBT), and Accelerated Bioeconomy Transformation (ABT)—are constructed using estimated elasticities and endogenous technology diffusion parameters. The findings indicate that under the ABT scenario, Gross State Value Added could expand to ₹34–35 lakh crore by 2050, reflecting a sustained growth premium of 2.3–3.1 percentage points relative to BAU. Concurrently, the transition is projected to generate 8–11 million additional jobs through labour-intensive bio-based value chains, alongside a 28–35% reduction in carbon intensity, indicating partial decoupling of growth from environmental pressures. However, these gains remain critically contingent upon institutional capacity, regulatory coherence, and inclusive value chain integration, underscoring the conditional nature of bioeconomy-led structural transformation.