Increasing urbanization degrades quantity, quality, and the functionality of spatial cohesion of natural areas essential to biodiversity and ecosystem functioning worldwide. The uncontrolled pace of building activity and the erosion of blue (i.e., aquatic) and green (i.e., terrestrial) landscape elements threaten existing habitat ranges and movability of wildlife. Local scale measures, such as nature-inspired engineered Blue-Green Infrastructure (BGI) are emerging mitigation solutions. Originally planned to promote sustainable stormwater management, adaptation to climate change and improved human livability in cities, such instruments offer interesting synergies for biodiversity in support of existing ecological infrastructure. BGI are especially appealing for globally declining amphibians, a rich and diverse vertebrate assemblage sensitive to urbanization. We integrated biological and highly resolved urban-rural land-cover data, ensemble models of habitat suitability, and connectivity models based on circuit theory to improve multi-scale and multi-species protection of core habitats and ecological corridors in the Swiss lowlands. Considering a broad spectrum of amphibian biodiversity, we identified distributions of amphibian biodiversity hotspots and four landscape elements essential to amphibian movability at the regional scale, namely i) forest edges, ii) wet-forest habitats, iii) soils with variable moisture and iv) riparian zones. Our work shows that cities can make a substantial contribution (e.g., up to 15% of urban space in the study area) to wider landscape habitat connectivity. We highlight the importance of planning BGI locally in strategic locations across urban and peri-urban areas to promote the permeability and availability of ‘stepping stone’ habitats in densely populated landscapes, essential to the maintenance of regional habitat connectivity and thereby enhancing biodiversity and ecosystem functioning.