Integrating conservation and natural resource management (CNRM) across international borders has been recognized as necessary to maintain biodiversity and ecosystem services in the face of broad-scale pressures including growing resource demands, invasive species, natural hazards, and climate change. Implementing transboundary CNRM strategies raises three prominent challenges: (1) engaging decision makers and stakeholders from local to regional scales and across borders; (2) linking local-scale management decisions to measureable objectives at landscape to regional scales; and (3) learning and adapting to the complexity of decision making under multiple objectives and scales. To address these challenges, we used a collaborative decision-analytic approach to support cross-border CNRM in multiple European transboundary protected areas (PAs) through the EU-funded ForAdapt project. The approach includes elements of structured decision making and has been applied in non-transboundary contexts and comprised iterative steps of identifying ultimate objectives, external factors (at least partly beyond control of the PA managers), resource allocation options, predictive model linking actions to the objectives, and the optimal allocation option. We applied and evaluated the approach for the first time in two transboundary conservation contexts. For the Triglav National Park (SL) and Prealpi Giulie Nature Park (IT) we identified a recommended 10-year transboundary resource allocation strategy for satisfying stakeholders concerned about brown bear and associated ecosystem services in the Julian Alps Ecoregion. We used participatory methods to develop a Bayesian decision network that accounted for competing stakeholder objectives and future uncertainties regarding perceived competence of the park managers and agreement among Alpine countries regarding bear management. The ultimate objectives were to maintain bear population carrying capacity and sustainable agriculture while minimizing stakeholder conflicts. The recommended allocation led to a concrete transboundary strategy for park managers to collaboratively engage stakeholders, data gatherers, and regional decision-makers in this transboundary pilot region for enhancing ecological connectivity under the Alpine Convention. The second case study focuses on Bavarian Forest National Park (DE) and Šumava National Park (CZ), which provides a recommended strategy for communication between and beyond parks regarding many of their CNRM activities. Together, these case studies demonstrate the efficiency of a collaborative decision-analytic approach for overcoming challenges of transboundary management and conservation for wildlife, biodiversity, and ecosystem services. Based on our own experience and independent feedback from stakeholders, we believe the approach will be useful in other transboundary CNRM contexts where there are already established working relationships between PA managers.