The transition to a sustainable bio-based economy is perceived as a valid path towards low carbon development for emerging economies that have rich biomass resources. In the case of Colombia, the role of biomass has been tackled through qualitative roadmaps and regional climate policy assessments. However, neither of these approaches have systematically addressed the complexity of the bio-based economy in the wider context of emission mitigation and energy and chemicals supply. In response to this limitation, we extended a bottom-up energy system optimization model by adding a comprehensive database of novel bio-based value chains. We included advanced road and aviation biofuels, (bio)chemicals, bioenergy with carbon capture and storage (BECCS), and integrated biorefinery configurations. A scenario analysis was conducted for the period 2015–2050, which reflected uncertainties in capacity for technological learning, climate policy ambitions, and land availability for energy crops. Our results indicate that biomass can play an important, even if variable, role in supplying 315–760 PJ/y of modern bio-based products. In pursuit of a deep decarbonization trajectory, the largescale mobilization of biomass resources can reduce the cost of the energy system by up to 11 billion $/y, the marginal abatement cost by 62%, and the potential reliance on imports of oil and chemicals in the future. The mitigation potential of BECCS can reach 24–29% of the cumulative avoided emissions between 2015 and 2050. The proposed system analysis framework can provide detailed quantitative information on the role of biomass in low carbon development of emerging economies.