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Industrial and urban symbiosis (IUS) is promoted as a strategy for advancing circular economy transitions, yet implementation often lags behind expectations. While most research highlights municipalities as facilitators of external partnerships, their internal governance role remains underexplored. The aim of this article is to examine how Swedish municipalities govern IUS within their own administrations. It applies a framework that combines governance modes with public sector organization (PSO) system elements, providing a structured lens for analyzing how internal organizational arrangements, roles, and routines shape the integration of IUS into municipal practice. The analysis draws on a qualitative case study of Malmö, based on nine interviews, complemented by seven interviews across six additional municipalities and a review of municipal strategies, plans, and policy documents. The material was analyzed through a deductive–inductive thematic approach in NVivo. Findings show that effective IUS governance seldom rests on a single instrument. Instead, it emerges from the interplay and sequencing of self-governing and authority-based strategies across organizational levels. Progress depended on how initiatives were connected to strategies, mandates, budgets, procurement routines, and coordination structures, allowing efforts to move beyond individual projects and become embedded in ordinary administrative practice. The study also identifies persistent tensions, particularly between municipalities acting as facilitators versus participants in symbiosis, and between internal circular practices and broader inter-organizational exchanges. The article contributes to IUS research by making visible the internal organizational dynamics through which governance modes operate in practice. By linking governance modes to PSO elements, the study clarifies how different parts of the municipal organization shape the direction and stability of IUS efforts. Practically, it suggests that governing IUS from within requires deliberate internal alignment so that strategic ambitions are consistently supported in decision-making and operational work.