If the stakes are high, policy researchers can find themselves under strong pressures from politicians or policy makers to compromise on issues like scope of a research project, research methodology, reporting, framing and interpretation of results, and timing of publication. Research organizations experiment with various formal and informal arrangements to cope with such pressures and guard their independence. This article describes six coping strategies that are being explored by the Netherlands Environmental Assessment Agency (PBL). These are: i) taking control in determining the project scope and the research questions; ii) making responsibilities explicit and guarding respective roles; iii) installing a broad based societal project advisory group; iv) having some researchers in a project that interact with stakeholders, while keeping others at a distance; v) having a differentiated communications strategy; vi) being fully transparent as to hypotheses and uncertainties regarding data and models. Safeguarding independence in research through formal rules and provisions is generally insufficient to protect research from undue stakeholder influence. Also changes in labor routines, relationship management and organizational cultures are needed, not only on the researcher side, but on the stakeholder side as well. This calls for dialogue and joint learning processes.