This study contributes towards a better understanding of learning dynamics in doctoral supervision by analysing how learning opportunities are created in the interaction between supervisors and PhD students, using the notion of experiencing variation as a key to learning. Empirically, we have based the study on four video-recorded sessions, with four different PhD students and their supervisors, all from life sciences. Our analysis revealed that learning opportunities in the supervision sessions concerned either the content matter of research (for instance, understanding soil structure), or the research methods—more specifically how to produce valid results. Our results illustrate how supervisors and PhD students create a space of learning together in their particular discipline by varying critical aspects of their research in their discussions. Situations where more open-ended research issues were discussed, created more complex patterns of variation. Both PhD students and supervisors can learn from this. Understanding of this mechanism that creates learning opportunities can help supervisors develop their competences in supervisory pedagogy.