This article explores the perceptions of Portuguese students enrolled in industrial doctorates, regarding potential conflicts that may arise from their supervision, their research topic and their research outputs. The study uses data collected from focus groups and subjected to content analysis. The findings suggest that industrial doctoral students recognise a divergence between university and industry, mainly regarding research outputs, and particularly industry's need to keep data confidential and the university's need to disseminate knowledge via the publication of articles. Convergence was noted at the level of joint supervision, sometimes facilitated by the fact that academics were also entrepreneurs. The success of this kind of collaborative doctorate depends on compromise between the two parties and on how students can manage this relationship. Therefore, their perspectives are an important source of information worth consideration.