Despite the growing importance and high priority assigned by the EU policy makers to the development of aquaculture, little attention has been given to analyze the economic performance of the sector at EU level. Recently, the profitability of the EU aquaculture sector has been estimated by the European Commission’s Scientific, Technical and Economic Committee for Fisheries (STECF). However, the few studies that have estimated the profitability of the EU aquaculture sector show sometimes divergent results. In this paper, the economic performance of the EU aquaculture sector is analyzed by country, segment and main species for the years 2006, 2009 and 2010 using financial and accounting data extracted from the Amadeus database and results are compared to other studies. This analysis helps to understand the methodological differences between the diverse sources. Moreover, this alternative methodology offers a simpler and faster alternative to the STECF’s profitability estimates of the aquaculture sector. The analysis indicates that after the economic downturn, companies started to recover profits in 2010 in almost all segments and countries, and that the highest profitability is recorded by companies in the marine segment as compared to freshwater and shellfish. © 2015, Springer International Publishing Switzerland.