EU studies extend into political science, political theory, public and foreign policy analysis, and international relations. The field's diversity speaks to different ontological, epistemological and methodological traditions and research practices. How the EU is conceived as a political reality and entity (ontology) tends to shape how researchers substantiate knowledge production about EU affairs (epistemology) and the way they uncover this knowledge (methodology), alongside choosing research methods and data. We argue that a ‘directional dependency’ exists between research ontology, epistemology, methodology and design. Using a meta‐analysis, we review EU politics research, mapping out directional dependencies in research design; how the paths operate; and deviations from those paths. We explore damaging effects of the research design process, evaluating how much this trap informs research in principle or in practice. We find that while in‐principle directional traps exist, research can be trapped to in‐practice dependencies, limiting the scope of innovation in the field.