Public administration research methodology should be flexible and comprehensive enough to include many methodologies and approaches to inquiry. In this paper we show how certain kinds of qualitative and mixed method studies often lack of a clear theoretical structure and as a result are poorly aligned across the stages of the research process. This paper introduces Working Hypotheses as a useful micro-conceptual framework with the capacity to address the alignment issue. It is particularly applicable to deductive case studies, which use qualitative or mixed methods. We show how positivism, postmodern and pragmatist philosophies shape quantitative, qualitative and mixed methods research. We also examine how types of reasoning (inductive, deductive and abductive) underlie approaches to research. The working hypothesis conceptual framework is introduced, placed in a philosophical context, defined, and applied to public administration and policy.