In mountain ecosystems, it is crucial to identify conservation strategies to avoid local extinctions mainly due to agropastoral abandonment. For this purpose, identifying appropriate system indicators is required, for example, butterflies, which respond precisely and quickly to environmental changes. Zerynthia polyxena is an ecotonal species of butterfly, and thus, through its conservation it could be possible to protect clearing and ecotonal species. To develop conservation measures, we set up a hierarchical investigation that characterizes the ecological preferences of the adult and larval Z. polyxena, and host plant—Aristolochia pallida—by collecting data on the butterfly abundance (adult and larvae), tree cover, and litter plant features and by phytosociological surveys. Adult preferences change along an altitudinal gradient; the highest butterfly presence is at sites with medium elevation (1100 m above sea level [asl]) with high presence of forest, but even sites at low elevation (975 m asl), a high presence of forest favors butterfly abundance. Larvae prefer partially shaded ecotone plots with abundant host plants and low management intensity (corresponding to abundant litter) and with heterogeneous tree cover. High tree cover (70%) at low altitude and low tree cover (<20%) at high altitude favor larval presence. Larvae prefer plants with large leaves. Host plants were more abundant at low elevation where tree cover was low (<20%). We found that the optimal ecological niches of host plant and larvae have a spatial mismatch. By analyzing vegetation dynamics and butterfly monitoring during one field season, we are able to describe current and past (about 10–50 years ago) management pressures, in order to identify butterfly ecological preferences in relation to local features and therefore to suggest local conservation actions that might support Z. polyxena, as well as other butterflies and insects. Specifically, management measures should prevent afforestation (e.g., through irregular mowing) and favor the presence of small clearings and of ecotonal habitats in relation to elevation. Our study suggests that a new multifunctional approach that combines local entomological and vegetational surveys could be applied to define species optimal habitat features and, thus, to address appropriate conservation measures.