The greatest challenge in accelerating the realisation of a sustainable and competitive bioeconomy is to demonstrate that enshrining sustainability principles at the very heart of a production line can generate value and improve its overall system. Strategies for reducing emissions, pollutants, indirect land use change or soil depreciation are all perceived as costs or necessary inconveniences to comply with stringent, climate change-focused policy frameworks. System dynamics modelling and competitive priorities are tools that can accurately and intelligently expand on the cross-value chain approach, which integrates both technical and environmental performances, to address the issue of harmonising sustainability and technical operations as one overall dimension of performance. A stock-and-flow model is developed to map a full biofuel value chain and quantitatively and coherently integrate factors of emissions, carbon, land, production, and technology. As such, environmental and operational impacts of innovative practices are measured, and subsequently linked to a qualitative framework of competitive priorities, as defined by transparency, quality, innovation and flexibility. Sustainability and productivity functions are found to reinforce each other when all competitive priorities are optimised. Equally, the framework provides a clear understanding of trade-offs engendered by value chain interventions. Advantages and limitations in the accessibility, scope and transferability of the multi-pronged analytical approach are discussed.