This chapter explores strategies for operationalising PhD studies in the context of a large research project addressing the unrelenting problem of ill-health in the growing population of informal settlements in the Global South. We advocate that PhD training presents an opportunity to contribute to these contexts by both training a new kind of action-oriented scholar, but also by strategically deploying the enormous energies and original work generated through PhD candidates towards this critical mission. Driven by the desire to give agency and utility to PhD researchers in a much-needed domain of transdisciplinary research, the chapter chronicles the trials of a group of four PhD candidates embedded in a large health study using innovative approaches to the revitalisation of 24 informal settlement communities in the Asia-Pacific. Through a discussion between the candidates and supervisory team, the chapter uncovers three types of embedded PhD’s. It articulates the challenges and opportunities of the model and reflects on the forces at play, producing practical advice for instrumentalising PhD research in the context of transdisciplinary research.