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The goal of achieving greenhouse gas emissions neutrality has intensified the search for fuels and chemicals from renewable sources. In this context, lignocellulosic biomass increasingly contributes to the transition to a bioeconomy. This chapter delves into the critical aspects of biomass processing, beginning with advanced pretreatment methods to improve sugar accessibility and routes for the efficient separation and purification of second-generation (2G) sugars. Bioproducts’ core challenges and competitiveness issues in current markets are explored, examining how life cycle assessment and techno-economic analysis can be leveraged to improve economic performance. Bioethanol and lactic acid have the highest commercial potential among the examples analyzed. The pivotal role of biofoundries and automation in transforming the life sciences sector, employing the Design-Build-Test-Learn (DBTL) framework within synthetic biology to expedite innovation, was underscored. The global evolution of biofoundries is presented through a bibliometric analysis, showcasing their impact on Industry 4.0 and the bioeconomy. The chapter concludes by emphasizing the interdisciplinary collaboration, policy support, and technological advancements required to harness the full potential of biofoundries and biorefineries. This comprehensive exploration highlights the need for innovation and strategic efforts to achieve sustainable development.