Several studies that have assessed the role of bioenergy in the energy system have primarily focused on electricity, heat, and road transport. However, sectors that have few alternatives to biomass, namely aviation and the chemical industry, are expected to become increasingly important. We have extended a bottom‐up energy systems model with fossil‐based and bio‐based chemicals and with renewable jet fuels to assess the deployment of biomass conversion technologies in the Netherlands until 2030. The model comprises detailed cost‐structures and mid‐term developments for the energy system with detailed cost‐supply curves for biomass, renewable energy technologies, and carbon capture and storage. The framework incorporates multi‐output processes, such as biorefineries, to address cross‐sectoral synergies. To capture the uncertainty in technical progress, technology development scenarios are used to assess cost‐optimal biomass utilization pathways over time. Slow technical progress (LowTech) leads to biomass applications for heating, first‐generation biofuels from hydrotreated oils, and bio‐based chemicals based on first‐generation fermentation systems. Enhanced technology development (HighTech) allows the production of second‐generation biofuels, large volumes of diverse bio‐based chemicals and renewable jet fuels. The required biomass may range from 230 PJ (LowTech) to 300 PJ (HighTech) in 2030, supplied primarily from imported resources. Both scenarios show that, under existing policies, CO2 emissions will only gradually be reduced to reach 1990 levels (140–145 Mt CO2). Further scenario analysis is recommended to assess model sensitivity and the necessary preconditions for future biomass conversion pathways and robust directions towards the required greenhouse‐gas mitigation pathways.