Doctoral training has changed in recent years with most PhDs now performed in structured programmes operated by university graduate schools. These schools generally superimpose a training framework onto the traditional research project to improve the education experience of the students and to prepare them for their careers. Many graduates progress to the commercial sector, where there is demand for highly skilled employees. The European Union (EU) promotes the development of transnational, training-focused, PhD programmes called Innovative Training Networks (ITNs) through Marie Skłodowska-Curie Actions. ITNs share many features of thematic PhD programmes, but they only recruit a single cohort of students, and they align with EU policy goals. These training networks are prestigious and very well regarded within European academia. The authors of this article were participants in a yeast biotechnology ITN, YEASTCELL, which finished in 2017. Some interesting insights into the more and less successful aspects of the project arose during discussions at the final project workshop. The views of the participants are distilled here in a discussion of how an ITN could be structured to maximise the benefits for the three main stakeholders: students, supervisors and industry partners.