Central to the exploitation of opportunities in entrepreneurial ecosystems (EEs) is the constant flow of resources within the ecosystem. While the local dependency of EEs nurtures knowledge creation and resource assembly, the regional nature of the ecosystem brings about limitations. However, the shifting perspectives of boundaries and expansion of scale fostered by digitalization have transformed interconnectedness and resource flows between actors and processes in EEs. Through a case study of the entrepreneurial ecosystem in the city of Jena in Germany, the challenges to resource flows in regional EEs and how these can be overcome through digitalization are examined. The findings show that the main challenge lies in inefficient ecosystem governance. Digitalization offers possibilities to enhance the flow of resources, albeit complementary to regional affordances.