In the regional studies of entrepreneurial activity, the ecosystem approach provides a means to identify factors that affect the behavior of business structures under shocks triggered by various reasons. The present work aims to clarify the nature of resilience, test the hypothesis about its cyclical nature, and assess it in different types of entrepreneurial ecosystems in border regions of Russia. In the study, the authors propose a theoretical four-phase model of the ecosystem resilience cycle. The two main characteristics—amplitudes of a downturn and an upturn—were identified; these characteristics were used to compare the resilience of ecosystems in border regions following the COVID-19 pandemic and increased sanctions in 2022. The study of the constructed cycles revealed that the sanctions caused a greater shock than the pandemic. Industrial ecosystems were found to be more susceptible to shocks than other ecosystems. Over the study period, export-oriented ecosystems exhibited greater revenue variation (26% to 74%), while for import-dependent ecosystems, revenue ranged from 13% to 63%. Foreign-invested ecosystems experienced severe shocks, with their revenue ranging from 15% to 98%. Despite this, the studied ecosystems show high resilience due to government support, reorientation to the markets of friendly countries, diversification of production, and increased intrasystem communication.