Urbanization is a global multidimensional process paired with increasing uncertainty due to climate change, migration of people, and changes in the capacity to sustain ecosystem services. This article lays a foundation for discussing transitions in urban governance, which enable cities to navigate change, build capacity to withstand shocks, and use experimentation and innovation in face of uncertainty. Using the three concrete case cities--New Orleans, Cape Town, and Phoenix--the article analyzes thresholds and cross-scale interactions, and expands the scale at which urban resilience has been discussed by integrating the idea from geography that cities form part of "system of cities" (i.e., they cannot be seen as single entities). Based on this, the article argues that urban governance need to harness social networks of urban innovation to sustain ecosystem services, while nurturing discourses that situate the city as part of regional ecosystems. The article broadens the discussion on urban resilience while challenging resilience theory when addressing human-dominated ecosystems. Practical examples of harnessing urban innovation are presented, paired with an agenda for research and policy.