In the 2005–06 season Yakimenko won the Budapest, Moscow, and Santiago World Cups. At the 2006 European Championships in İzmir he edged past Romania's Florin Zalomir in the semi-finals, then defeated Ukraine's Volodymyr Lukashenko to earn his first European individual title. In the team event Yakimenko was trusted to close the matches, a role Pozdnyakov had fulfilled for ten years. Another change was the line-up of young Nikolay Kovalev. Russia were narrowly beaten by Romania in the semi-finals, but prevailed over Belarus to win the bronze medal. In the World Championships Yakimenko was defeated in the first round by Belarus' Aliaksandr Buikevich. Russia's director of fencing Sergey Kolganov attributed this below-par performance to overtraining and mental exhaustion after a long season. Yakimenko finished the season No.4.