A quarter-final in the 2013 Moscow World Cup was a good sign for the new season, but a sprained ankle during the Akropolis Cup in Athens caused him to miss the most of it. He was not fully recovered for the European Championships in Zagreb, but he managed to reach the final despite a difficult bout in the quarters against Italy's Diego Occhiuzzi. Defeated by Romania's Tiberiu Dolniceanu, he came away with a silver medal. In the team event, top seed Russia, further handicapped by Nikolay Kovalev's knee injury, suffered a shock defeat to Ukraine in the quarter-finals and finished 7th. Yakimenko later explained that the newly formed team was still in its running-in period and identified Andriy Yagodka's long arm as the main cause of their problems. He chose not to attend the 2013 Summer Universiade to preserve his form for the World Championships in Budapest. His ambitions were however cut short in the second round by Romania's Alin Badea. In the team event Russia prevailed over reigning Olympic champion South Korea, then defeated Romania to take the gold medal. Yakimenko finished the season No.16, his worst ranking since 2003–04, and was not selected for the 2013 World Combat Games in St-Petersburg.