Entrepreneurial Ecosystems (EEs) have been gaining relevance as a comprehensive framework to guide the promotion of entrepreneurship and innovation, as well as to foster local socio-economic development. In the case of rural areas, the locational disadvantages lead to several bottlenecks that hinder entrepreneurs’ capacity to develop their businesses. Thus, for overcoming these bottlenecks by accessing resources from other ecosystems is crucial to the sustainable development and resilience of rural entrepreneurs and EEs. The underlying proposition of this study is that EEs are not confined to specific geographic boundaries but are embedded in multi-layered dynamics that extend beyond local regions. Through an empirical analysis of three rural EEs in Portugal, this paper explores the role of the local governments in facilitating trans-local linkages and the significance of these processes in mitigating local bottlenecks.