Doctoral students and faculty members sometimes face unexpected barriers when engaging in qualitative research that can impede career advancement. In part, this can be because qualitative methodologies often conflict with objectivist epistemological assumptions that are deeply embedded in university cultures. Since ontology, epistemology, methodology, and methods are related, it is imperative for qualitative researchers to understand these differences and recognize the resulting tensions. Furthermore, when conducting qualitative research it is critical to design studies in which the epistemology, methodology, and methods are logically integrated for the best quality work. In this article, I seek to make transparent the link between everyday problems that arise (in dissertation defenses, funding and Institutional Review Board applications, peer review, tenure and promotion, etc.) and the underlying epistemological and methodological issues that produce them. I seek to educate beginning qualitative researchers about the importance of this integration in their own work and to arm them with some diagnostic skills. In doing so they will be better prepared to successfully negotiate the politics of science, the politics of evidence, and the politics of methods within their home institutions.