Today we are facing many politically driven sustainability transitions in complex sociotechnical systems. Sustainability transition scholars look at these transitions with their own theoretical lenses, often paying too little attention to the interactions of power, politics and agency. While simulation is a useful method to address the complexity of long-term sustainability transitions, the number of transition studies using simulation is limited, as the field is still dominated by the use of qualitative case studies. This has recently been recognized by transition scholars, advocating various levels of integration of case studies, theoretical frameworks and simulation methods. However, a process to support the development of coherent and conceptually compatible mixed-methods research design is still missing. Furthermore, modeling and simulation studies are often lacking the theoretical foundations to model the intricacies of transitions at the micro-level, due to a lack of formalized transition frameworks at a low level of abstraction. In this thesis three methodological contributions are made towards modelling endogenous policy-emergence in societal transitions. First, system dynamics simulation is proposed as a method to perform a meta-analysis of Swiss energy transition scenarios, providing new insights in system level uncertainty and sensitivity, as well as policy levers. Second, a mixed-methods process model is developed based on a comprehensive literature review of sustainability transitions studies. The process model addresses the theoretical and conceptual compatibility of prominent transition frameworks and relevant simulation paradigms, facilitating the design and reporting of coherent mixed-methods research designs. Third, a formalization of the multi-level perspective is developed at the level of agents to better address the role of individuals in sustainability transitions, as well as to internalize policy-making. The presented formalization refines and extends the closely related concepts of power, agency and politics.