Urban biodiversity is critically undermined by the loss and mismanagement of habitat trees—living or dead trees that provide essential microhabitats for highly specialized organisms. Although urban tree planting initiatives are widely promoted, urban forests often lack age diversity, with mature and senescent trees being rare or absent.In our research project, we monitored biodiversity associated with different urban trees across two study areas in Italy (Milano and Pesaro) and investigated the biological communities associated with habitat trees by assessing biodiversity across multiple taxonomic groups. Biodiversity was studied to address the question of what contribution habitat trees and the micro-niches they provide make to habitat provisioning for biodiversity. Abundance and diversity were therefore analyzed across the full height of the tree in order to describe patterns of vertical distribution. Our findings demonstrate that habitat trees support a high abundance and diversity of invertebrate communities, including rare and protected species, many of which depend on specific microhabitats and vertical patterns exists. This evidence highlights that urban tree management interventions can have substantial and often underestimated ecological impacts. For example, simplifying tree structure with damaging pruning techniques or reducing tree height can negatively impact urban biodiversity. In response, we propose integrating ecological criteria into arboricultural practice and urban policy related to green infrastructure by developing standardized approaches for identifying, mapping, and retaining habitat trees. Such approaches support the creation of ecological networks and promote uneven-aged urban forests as a strategy for long-term resilience. We further emphasize key conceptual tools for policy and practice, including ecological non-substitutability, net benefit assessment in tree management, and others. We argue that effective nature restoration in urban environments must explicitly include the conservation of habitat trees, as these structures are ecologically non-substitutable in the short to medium term and they biodiversity they sustain cannot persist in poorly structured urban forests.