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The methodological discourse of mixed-methods research offers general procedures to combine quantitative and qualitative methods for investigating complex fields of research such as higher education. However, integrating different methods still poses considerable challenges. To move beyond general recommendations for mixed-methods research, this chapter proposes to discuss methodological issues with respect to a particular research domain. Taking current studies on the transition to higher education as an example, the authors first provide an overview of the potentials and limitations of quantitative and qualitative methods in the research domain. Second, they show the need for a conceptual framework grounded in the theory of the research object to guide the integration of different methods and findings. Finally, an example study that investigates transition with regard to the interplay of the individual student and the institutional context serves to illustrate the guiding role of theory. The framework integrates different theoretical perspectives on transition, informs the selection of the research methods, and defines the nexus of the two strands that constitute the mixed-methods design. As the interplay of individual and context is of concern for teaching and learning in general, the example presented may be fruitful for the wider field of higher education research.