Global change drivers, including fragmentation, climate change and habitat degradation, are accelerating the alarming decline in biodiversity worldwide. Additionally, biodiversity-environment interactions may vary depending on the spatial scale, as communities are shaped by both large- and small-scale factors. Therefore, it is crucial to assess the taxonomic, functional and phylogenetic responses of communities to environmental factors operating at different scales. To address this, we investigated epiphytic lichen communities thriving in 20 oak forest fragments located between temperate and Mediterranean climates in the northwest of the Iberian Peninsula. Using structural equation modelling, we tested the effects of forest fragmentation, climate, habitat structure and quality on functional (FD), taxonomic (TD) and phylogenetic (PD) diversities at plot and tree scales, considering both direct and indirect effects mediated through FD. Our findings indicate that habitat structure and climate are key determinants of diversity at both spatial scales. Additionally, habitat quality emerged as a critical predictor exclusively at the tree scale. Heterogeneity in habitat structure had a profound effect on diversity, increasing FD, TD and PD, while climate primarily influenced TD. Conversely, habitat quality positively affected both FD and TD, but its net effect on PD was negative. Although TD can be inferred through PD, FD emerged as the cornerstone mediating between the environment and other diversity facets. However, direct relationships were also identified. These results highlight the necessity of incorporating multi-scale and multi-faceted approaches in forest management practices. Effective forest management should monitor and manage key factors such as slope and DBH to enhance FD, TD, and PD of lichens. By focusing on these factors, forest management can ensure the resilience and sustainability of forest ecosystems, promoting biodiversity conservation and ecosystem services in the face of global environmental changes.