Anonymisation processes are an embedded, if contested, element of ethical research practice. Current debates, highlighting various challenges to anonymity, suggest the importance of situated ethics and negotiated solutions. However, the strategies adopted are necessarily mediated by the researcher's epistemological positions. Longitudinal studies with their extended timeframes and intensive research relationships tend to amplify ethical dilemmas and highlight the contingency and fluidity of ethical processes. Here we explore how temporality intersects with epistemology in a qualitative longitudinal (QL) study of organisations located in a contemporary policy context. We reflect on the confidentiality and anonymity dilemmas that develop and change over time, the strategies adopted and the implications of these for the type of knowledge produced. We suggest that QL studies entail flexibility within epistemological frameworks. These issues have particular resonance and consequences for researchers in light of contemporary pressures around public scrutiny of academic performance and wider debates around public sociology.