In 2005-06 (when the competition changed format) AEL passed the first group round by finishing second, eliminating PAOK BC and Kallev Tallinn and reaching the second round (round of 16).
Unlike the previous year when AEL finished with 0 points in the second round, being in the same group with CB Estudiantes, Liege Basket and BC Šiauliai, they finished second with 5 victories and 1 defeat - tied with the Estudiantes because of the matches between them.