Some value chains (VCs) currently represent bioeconomy systems through which countries have opportunities for development and growth. However, not all bioeconomy systems guarantee sustainability. Multiple VCs aimed at food production can have small and high-scale levels. Although high-scale VCs are viable, at least from an economic perspective, it has more economic revenues to the owners, diluting the benefit to producers. In the case of small-scale VCs, improvements can have a greater impact on sustainability since the beneficiaries are not only the enterprises (producers and processors) but also, at a social level, a better redistribution of value chain profits for the small communities is involved. In addition, the quality of products in small-scale VCs may use fewer chemical inputs and generally have more environmentally friendly processes. However, in the small-scale VCs, residues are generated that must be fully used through the biorefinery concept, further improving the sustainability of these VCs in mainly rural areas. This chapter describes the concepts of VCs in the bioeconomies framework, with Colombia as a case study. The potential of small-scale VCs is demonstrated, along with the possibility to integrate VCs through sustainability assessment.