The idea that cities are self-organizing systems, and that the state has a limited capacity to control and shape them, has gained momentum in the last decade among planning professionals, designers and politicians. Recent political discourse on new localism and liberal individualism builds on a similar understanding of cities, giving responsibility to citizens and their collective associations in light of state rescaling. The consequences of such perspectives for urban development have yet to be conceptualized. This article proposes a critique of the use of self-organization in policy practice, building on the argument that this concept destabilizes two constitutive categories of urban intervention: spatial boundaries and temporal programmes. In so doing, self-organization conveys two peculiar understandings of agency in city-regional spaces and of urbanity: the disaggregation of city-regions and the deconstruction of urbanity. Looking at the recent change in Amsterdam’s urban development practice, I show that, while self-organization is used to emphasize that city-regions constitute interconnected systems of dynamics, when applied in policymaking it in fact leads to the disaggregation and fragmentation of urban regions. Moreover, while the capacity of self-organization to deconstruct codified notions of urbanity that frustrate urban relations is often celebrated, its use in policy produces newly exclusive urban fabrics.