During the 2016–17 Four Hills Tournament, he achieved a second place twice, in Oberstdorf and Garmisch-Partenkirchen. In the trial before the competition in Innsbruck, Stoch fell while landing after a long-jump. He had a very painful shoulder injury and hematoma. Despite the injury, he continued to participate in the tournament. In windy competition in Innsbruck he took fourth place, and for the overall was second with a loss to leader Daniel Andre Tande 1.7 points. On 6 January 2017 he won the last competition in Bischofshofen and won overall (997.8 points) with a predominance over the second overall Piotr Żyła 35.3 points. Since Bischofschofen, Stoch won two individual competitions in Wisła and one in Zakopane. He has not lost since for individual competitions. In Zakopane Polish team, including Stoch and teammates – Kubacki, Kot, Żyła achieved second place in team competition. On 28 January 2017 Poland won their second team competition in history in Willingen.