Abstract Due to the central role of landscape connectivity in many ecological processes, evaluating and accounting for it has gained attention in both theoretical and applied ecological sciences. To address this challenge, researchers often use generic species to simplify multi‐species connectivity assessments. Yet, this approach tends to oversimplify movement behaviour, likely reducing realism and precision of connectivity model outputs. Also, the most widely used methods and theories for assessing landscape connectivity, namely circuit and network theories, have strong limitations. Finally, uncertainty or robustness estimates are rarely integrated in connectivity assessments. Here, we propose a versatile framework, which, instead of using arbitrary defined generic species, first identifies species groups based on species' environmental niches and morphological, biological, and ecological traits. Second, it combines circuit and network theories to take the best of the two methods to assess landscape connectivity for those groups, while integrating uncertainties in modelling choices. Specifically, ecological continuities (i.e. landscape elements contributing to connectivity) are calculated for these groups and used together with group dispersal capacities to derive network‐based connectivity metrics for conservation areas. We detailed our framework through a case study where we assess the connectivity of 1619 protected areas in metropolitan France for 193 vertebrate species. Our study revealed that both the protection of ecological continuities and the connectivity of protected areas for 11 mammal and 19 bird groups, respectively, were quite low, with variations among groups. Different protection types (i.e. national parks, reserves or prefectural orders) contributed unequally to the overall connectivity of group‐specific suitable habitats. Considering uncertainty propagation was crucial, as many connectivity metrics varied among repetitions. The proposed framework combines different connectivity tools to provide a more relevant and comprehensive assessment of landscape connectivity. It can be used to inform the decision‐making process for spatial planning, particularly in the context of connectivity conservation and management, or support theoretical studies to better understand the ecological role of landscape connectivity. Its flexibility allows easy application under various environmental conditions, including future scenarios.