Biomass, bioenergy and negative emission technologies are inherent to the future design of energy systems. Urban clusters have a growing demand for fuel, heat and electricity, which is both a challenge and an opportunity for biomass-based technologies. Their deployment should meet demand, while minimizing environmental impact and staying cost-competitive. We develop a systematic approach for the design, evaluation and ranking of biomass-to-X production strategies under uncertain market conditions. We assemble state-of-the-art and innovative conversion technologies, based on feedstock, by-products and waste characteristics. Technical specifications, as well as economic and environmental aspects are estimated based on literature values and industry experts input. Embedded into a bi-level mixed-integer linear programming formulation, the framework identifies and assesses current and promising strategies, while establishing the most robust and resilient designs. The added value of this approach is the inclusion of sub-optimal routes which might outperform competing strategies under different market assumptions. The methodology is illustrated in the anaerobic digestion of food and green waste biomass used as a case study in the current Swiss market. By promoting a fair comparison between alternatives it highlights the benefits of energy integration and poly-generation in the energy transition, showing how biomass-based technologies can be deployed to achieve a more sustainable future.