Transitions research has gained traction in sustainability studies for its systemic approach to environmental challenges. A central tenet is that the persistence of these challenges can be attributed to ‘system failures’, and that system innovation is needed, i.e. a multitude of innovations that co-evolve into system-wide transformations. However, many contrasting views of ‘systems’ and ‘systemic frameworks’ are seemingly always clamouring for attention, whilst it is not always clear what they’re referring to. Taking a reflexive methodology approach, this chapter addresses recurring questions: Transforming ‘systems’: Which? How? Whose? Why? Whither? Whence? For instance, is transitioning the ‘mobility system’ a matter of electrification or of unlearning car dependency? In transitioning the ‘energy system’, is importation of rare minerals a central part or an externality? The chapter presents a methodological overview of systems analysis in transitions research. It brings out how transitions research has developed a fine sense of Critical Systems Thinking. On the other hand, it also shows the need for further methodological reflection on the study of transitioning ‘systems’.