Botanical gardens are dynamic systems of high scientific, ecological, cultural, and historical value. They are irreplaceable places to cultivate, manage, study, and preserve tree diversity. One of the ongoing biggest challenges worldwide in managing and preserving trees is climate change, which exposes specimens to more stressful and severe environmental conditions, causing an increase in mortality. In our research, we aimed to assess the future climate change impact on the tree collection of Botanic Garden of Pisa in order to outline the expected consequences about tree cultivation and management. Under the most pessimistic scenario, in 2090 more than 60% of the tree species cultivated in the Botanic Garden of Pisa are expected to fall outside of their climatic niche. Future chances and pitfalls in managing urban green areas, focusing on the botanical garden community, are also explored.