The process of European integration resulted in a marked increase in transnational economic flows, yet regional inequalities along many developmental indicators remain. We analyze the unevenness of European economies with respect to the embedding of export sectors in upstream domestic flows and their dependency on dominant export partners. We use the WIOD dataset of sectoral flows for the period of 1995–2011 for 24 European countries. We found that East European economies were significantly more likely to experience increasing unevenness and dependency with increasing openness, while core countries of Europe managed to decrease their unevenness but increased their openness. Nevertheless, by analyzing the trajectories of changes for each country, we see that East European countries are also experiencing a turning point, either switching to a path similar to the core or to a retrograde path with decreasing openness. We analyze our data using pooled time series models and case studies of country trajectories