Sustainability assessment of biodiesel production is a topic of increasing importance due to the interest of governments to stablish sovereignty strategies, diversify their energy matrix and set up the impact of biofuels production. In this context, this work proposes a system dynamic model to assess biodiesel production in a specific context, based on a general hierarchical structure of sustainability assessment that integrates dimensions of sustainable development with principles, criteria and indicators (PC&I). The assessment framework of biodiesel production was defined based on a comprehensive state of the art, resulting in a selection and analysis of 113 documents, including laws, directives and other normative documents, policy documents, certificates and papers published in peer-reviewed journals. To define the final framework, a validation strategy based on expert survey consultations and a descriptive statistical analysis was conducted. As a result, a framework composed of five dimensions (social, economic, environmental, political and technological), 13 principles and 31 criteria was proposed. Subsequently, a System Dynamics (SD) model was developed and applied for assess the sustainability biodiesel production in Colombia. Initially, the SD model was used to simulate the biodiesel production considering the current conditions in Colombia, enabling to determine the baseline (years 2008 to 2014). Subsequently, some exogenous indicators of the baseline scenario were modified in order to generate a sensibility analysis to define several fundamental conditions for the sustainable biodiesel production in the Colombian context. Once the sensibility analysis was conducted, the conditions that promote or discourage biodiesel production were determined and, consequently, optimistic and pessimistic scenarios were proposed. The results of the analysis of the scenarios can help institutions, decision-makers and other agents related to establish the conditions to be carried out to promote a sustainable biodiesel production