Ilinykh/Katsalapov started their season with gold at the 2012 Crystal Skate of Romania. They won silver at their first 2012–13 Grand Prix event, the 2012 Rostelecom Cup. At the 2012 NHK Trophy, Ilinykh/Katsalapov were third after the short dance. Ilinykh fell ill before the free dance due to food poisoning but went on to compete. They placed second in the segment and won the silver medal. They qualified for the 2012 Grand Prix Final in Sochi, Russia, and finished sixth at the event. At the 2013 Russian Championships, Ilinykh/Katsalapov won the silver medal behind defending national champions Ekaterina Bobrova / Dmitri Soloviev. At the 2013 European Championships, they placed second in the short dance and first in the free dance. They won the silver medal, just 0.11 of a point behind gold medalists Bobrova/Soloviev. Ilinykh/Katsalapov finished 9th at the 2013 World Championships.