The transition from primary to secondary education is regarded as a crucial phase in pupils’ school careers. Changes in the school environment have a negative influence on pupils’ perceived control and engagement. However, until now little attention has been devoted to the role of the onset of ability grouping therein, which often coincides with the start of secondary education. Research has shown that students in non‐academic tracks display lower levels of perceived control and engagement. In this study we examine the relation between pupils’ prospective track choice and feelings of perceived control and behavioural and cognitive engagement before the transition to secondary education. Stepwise multilevel regression models were run on data collected from pupils in their last year of primary education in 36 schools in the cities of Antwerp and Ghent (Flanders, Belgium) in May–June 2016. The results show that pupils who indicated that they would start secondary education in non‐academic tracks displayed lower levels of perceived control and behavioural and cognitive engagement than pupils who indicated that they would start in an academic track. Further analyses suggest that teacher assessments of pupils’ competence play an important role in explaining these differences according to prospective track choice—with regard to perceived control and behavioural disengagement, this effect is established net of students’ actual competence. This study demonstrates that differences in perceived control and engagement according to track originate in primary education, and that primary school teachers play a vital part in labelling students according to their future careers.