Stakeholder participation is advocated widely, but there is little structured, empirical research into its influence on policy development. We aim to further the insight into the characteristics of participatory policy development by comparing it to expert-based policy development for the same case. We describe the process of problem framing and analysis, as well as the knowledge base used. We apply an uncertainty perspective to reveal differences between the approaches and speculate about possible explanations. We view policy development as a continuous handling of substantive uncertainty and process uncertainty, and investigate how the methods of handling uncertainty of actors influence the policy development. Our findings suggest that the wider frame that was adopted in the participatory approach was the result of a more active handling of process uncertainty. The stakeholders handled institutional uncertainty by broadening the problem frame, and they handled strategic uncertainty by negotiating commitment and by including all important stakeholder criteria in the frame. In the expert-based approach, we observed a more passive handling of uncertainty, apparently to avoid complexity. The experts handled institutional uncertainty by reducing the scope and by anticipating windows of opportunity in other policy arenas. Strategic uncertainty was handled by assuming stakeholders’ acceptance of noncontroversial measures that balanced benefits and sacrifices. Three other observations are of interest to the scientific debate on participatory policy processes. Firstly, the participatory policy was less adaptive than the expert-based policy. The observed low tolerance for process uncertainty of participants made them opt for a rigorous “once and for all” settling of the conflict. Secondly, in the participatory approach, actors preferred procedures of traceable knowledge acquisition over controversial topics to handle substantive uncertainty. This excluded the use of expert judgment only, whereas the experts relied on their judgment in the absence of a satisfactory model. Thirdly, our study provides empirical evidence for the frequent claim that stakeholder involvement increases the quality of the knowledge base for a policy development process. Because these findings were obtained in a case that featured good process management and a guiding general policy framework from higher authorities, they may not generalize beyond such conditions.