Increasing urbanisation calls for careful landscape conservation planning to maintain biodiversity in urban areas. Urbanisation not only decreases the amount and quality of habitats, but it also affects habitat connectivity, which is crucial for species’ long-term persistence. The mitigation hierarchy approach of avoiding, reducing and offsetting the negative impacts of development projects is a powerful tool to prevent biodiversity loss. However, this process is typically used at the local scale and on a project-by-project basis, ignoring the cumulated effects of several projects on habitat connectivity. We applied a landscape-level approach to the mitigation hierarchy to achieve no net loss of connectivity during urban planning. Using spatial graphs, we assessed avoidance, reduction and offsetting scenarios for mitigating the impact of ten urban development projects in the city of Jyväskylä, Finland, here focusing on the habitat network of the endangered Siberian flying squirrel (Pteromys volans). We found a negative impact of urban development on network connectivity and prioritised habitat patches and corridors, which should be maintained to avoid and reduce the impacts. The no net loss of connectivity was achieved by adding new habitat patches in locations that maximise connectivity. We also found that the results were highly sensitive to variations in the dispersal distance of the focal species used in the connectivity model. An inadequate reference value for this parameter may lead to underestimation of the impacts of development projects and, therefore, insufficient mitigation actions. With a case study, we showed that spatial graph analysis can support decision-making by identifying and prioritising the actions needed to maintain habitat connectivity in urban landscapes.