Maximising research productivity is a major focus for universities world-wide. Graduate research programs are an important driver of research outputs. Choosing students with the greatest likelihood of success is considered a key part of improving research outcomes. There has been little empirical investigation of what factors drive the outcomes from a student's PhD and whether ranking procedures are effective in student selection. Here we show that, the research environment had a decisive influence: students who conducted research in one of the University's priority research areas and who had experienced, research-intensive, supervisors had significantly better outcomes from their PhD in terms of number of manuscripts published, citations, average impact factor of journals published in, and reduced attrition rates. In contrast, students' previous academic outcomes and research training was unrelated to outcomes. Furthermore, students who received a scholarship to support their studies generated significantly more publications in higher impact journals, their work was cited more often and they were less likely to withdraw from their PhD. The findings suggest that experienced supervisors researching in a priority research area facilitate PhD student productivity. The findings question the utility of assigning PhD scholarships solely on the basis of student academic merit, once minimum entry requirements are met. Given that citations, publication numbers and publications in higher ranked journals drive university rankings, and that publications from PhD student contribute approximately one-third of all research outputs from universities, strengthening research infrastructure and supervision teams may be more important considerations for maximising the contribution of PhD students to a university's international standing.