In researching student writing in the context of higher education, it is considered good practice to combine analysis of students’ written texts with discourse-based interviews, where the researcher questions student participants about their rhetorical choices in writing. In this way, the researcher’s interpretation of the students’ textual features can be further supported by the students’ own reported intentions, thus compiling a fuller picture of the writing. However, in practice, this method could contain several issues regarding methodological soundness, practical implementation of the interviews and data interpretation. This paper will draw on a doctoral research project into students’ citation practices to discuss three challenges that emerged before, during and after the discourse-based interviews: selection of the citation instances in texts to discuss in interviews, probing into students’ real perceptions without influence from pre-existing theories and connecting the text analyses results with interview data during the data analysis stage. Mitigating solutions that were adopted in the project will also be discussed. Such discussions can hopefully inform future studies that intend to combine text analysis with discourse-based interviews.