Structured doctoral education is increasingly preferred compared to the individual model. Several science policy organisations give recommendations on how to structure doctoral education. However, there is little research on to what extent these recommendations find their way into practice. In our study, we first compared European and German recommendations on doctoral education with, second, the institutional regulations of structured doctoral programmes (N = 98) in the life sciences at twelve different German universities. Additionally, we third asked doctoral graduates (N = 1796) of these structured doctoral programmes and graduates of individual doctoral studies about their experience in doctoral education. Fourth, we contrasted the regulations of structured doctoral programmes with the reported experiences of their graduates. We found significant deviations of the reported practices of graduates from the regulations of their organisations, regarding the student admission, supervision and curricular activities of doctoral candidates. The efficacy of structured versus traditional doctoral education should be examined based on reported practice rather than on the respective written regulations.