ENThis article reveals the main challenges that occur in the context of Central and Eastern European countries and presents a theoretical framework that reflects the ecosystem‐based approach to the bottom‐up emergence of industrial ecosystems. The framework that adapts the approach of complexity theory was created by analysing success stories of the (re)emergence and development of self‐organising industrial systems. Based on the analysis of those stories, the integrated stages of emergence and development were defined. The framework presented in this article allows researchers and practitioners to identify the main obstacles that hinder the development of industrial ecosystems in any stage. In addition, this framework facilitates the formulation of strategies behind the successful regional industrial systems, including the context of Central and Eastern European countries.