For decades, from design theory to urban planning and management, from social sciences to urban environmental science, cities have been probed and analyzed from the partial perspective of single disciplines. The digital era, with its unprecedented data availability, is allowing for testing old theories and developing new ones, ultimately challenging relatively partial models. Our community has been in the last years providing more and more compelling evidence that cities are complex systems with emergent phenomena characterized by the collective behavior of their citizens who are themselves complex systems. However, more recently, it has also been shown that such multiscale complexity alone is not enough to describe some salient features of urban systems. Multilayer network modeling, accounting for both multiplexity of relationships and interdependencies among the city’s subsystems, is indeed providing a novel integrated framework to study urban backbones, their resilience to unexpected perturbations due to internal or external factors, and their human flows. In this paper, we first offer an overview of the transdisciplinary efforts made to cope with the three dimensions of complexity of the city: the complexity of the urban environment, the complexity of human cognition about the city, and the complexity of city planning. In particular, we discuss how the most recent findings, for example, relating the health and wellbeing of communities to urban structure and function, from traffic congestion to distinct types of pollution, can be better understood considering a city as a multiscale and multilayer complex system. The new challenges posed by the postpandemic scenario give to this perspective an unprecedented relevance, with the necessity to address issues of reconstruction of the social fabric, recovery from prolonged psychological, social and economic stress with the ensuing mental health and wellbeing issues, and repurposing of urban organization as a consequence of new emerging practices such as massive remote working. By rethinking cities as large‐scale active matter systems far from equilibrium which consume energy, process information, and adapt to the environment, we argue that enhancing social engagement, for example, involving citizens in codesigning the city and its changes in this critical postpandemic phase, can trigger widespread adoption of good practices leading to emergent effects with collective benefits which can be directly measured.