CONTEXT The urgency of redesigning the way food is produced and consumed has implications for the systems perspective of agronomy. An increasingly important strain of research addresses the ‘how-to’ question associated with the transformation of ‘maldesigned’ agricultural systems and produces ‘transformative knowledge’ as part of transitions in-the-making. Such knowledge production goes beyond ‘transformation knowledge’ resulting from the more classical analytical agronomic approaches and stances. Contributing to transitions in-the-making thus calls for systems agronomists to question their profession's why, what, and how. OBJECTIVE This special issue brings together contributions by systems agronomists collaborating with other scientists and societal actors revealing the less visible stream of fine-grained work to support transitions in-the-making in agroecosystems. METHODS In this introductory paper, changes in research scope and methods emerging from the contributions are highlighted to reinforce the engaged systems agronomist's roles in contributing to food system transitions. RESULTS AND CONCLUSIONS Three results stand out: 1) Contributing to transitions in-the-making necessitates going beyond analysis-oriented research stances to address the ‘how’ of transformative knowledge, and move beyond the more time-efficient dominant ‘what’ and ‘why’ questions; 2) Meta-methods are emerging about how to adapt and embed existing agronomic knowledge products within change processes. Reflection on the overarching transformation dynamics and on how to articulate knowledge products and change process will constitute an important extension of the systems agronomist's methods; 3) The efficacy of scientific transformative knowledge development may be enhanced if the notion of design is used more strictly in relation to engagement in societal change. SIGNIFICANCE The need to respond to the how-to questions associated with the transformation of the way food is produced and consumed requires systems agronomists to reflect on their stance in the research process, the way they design their research inclusively, and the way they shape their methods. This Special Issue provides promising examples of the (re-)emerging strain of engaged systems agronomists.