Conservation resource allocation involves a complex set of considerations including species, habitats, connectivity, local to global biodiversity objectives, alternative protection, and restoration actions while requiring cost-efficiency and effective implementation. We present a national-scale spatial conservation prioritization analysis for complementing the network of protected mires in Finland. We show how spatial prioritization coupled with regional targets and expert knowledge can facilitate structured decision-making. In our application, a discussion between experts was structured around the prioritization model enabling integration of quantitative analysis with expert knowledge. The used approach balances requirements of many biodiversities feature over large landscapes while aiming at a cost-effective solution. As a special analytical feature, mire complexes were defined prior to prioritization to form hydrologically functional planning units, including also their drained parts that require restoration for the planning unit to remain or potentially increase in value. This enabled selection of mires where restoration effort is supporting and benefitting from the core mire areas of high conservation value. We found that a key to successful implementation was early on structured co-producing between analysts, mire experts, and decision-makers. This allowed effective multidirectional knowledge transfer and evaluation of trade-offs related to the focal conservation decisions. Quantitative trade-off information was seen especially helpful by the stakeholders to decide how to follow the analysis results. Overall, we illustrate a realistic and applicable spatial conservation prioritization case supporting real-world conservation decision-making. The introduced approach can be applied globally to increase the effectiveness of large-scale protection and management planning of the diverse wetland ecosystem complexes.