Cities continue to grow worldwide, and the highly modified urban landscape becomes an inhospitable environment for many species because the natural vegetation cover is commonly fragmented, and the remnants are often isolated. Protected Areas (PAs) located surrounding or within urban areas may not achieve their goal of protecting local or regional biodiversity. Thus, an urban ecological network is essential to support their PAs. Thus, this study aimed at assessing the PAs connectivity in an urban landscape in Brazil and understanding whether urban forest fragments can support an urban ecological network. Besides spatial models based on functional connectivity and graph theory, we used participatory techniques to design the resistance surface and the least-cost paths (LCPs) for Atlantic Forest birds. The results showed critical paths (LCPs), important areas for restoration programs for improving PAs connectivity, and essential forest fragments for conservation and restoration. Although the landscape has a forest structure with 1873 forest fragments and 516 links through which the LCPs were structured, most forest fragments and LCPs cannot provide the necessary support for the PAs connectivity. The current ecological network is dependent on forest fragments neighboring (outside PAs) and the flux dispersions occurred mainly in the peri-urban areas. Riparian zones and anthropic grasslands also showed importance for the PAs connectivity. We identified only 28 forest fragments spatially connected, presenting several sizes, and located near large forest areas, relevant PAs, and riparian zones. Six of these forest fragments, smaller than ten hectares and strategically located in the urban matrix, were indicated for restoration actions. The current low connectivity among PAs brings the importance of native vegetation restoration in the riparian zone and anthropic grassland and the importance of the periurban areas to promote biodiversity connectivity in the urban landscape.