In the 2016 season, Shoji started the season when he helped Kashima Antlers keep two clean sheets in the first two league matches of the season. Since the start of the season, Shoji continued to regain his first team place, playing in the centre–back position. It wasn't until on 6 April 2016 when he scored his first goal of the season, in a 3–1 win against Nagoya Grampus in the J.League Cup. By the end of the J.League first stage, Shoji's contribution to the first team helped the side finish at the top of the table. After serving a one match suspension, he made his return to the starting line-up, as Kashima Antlers lost 3–1 loss against Gamba Osaka on 2 July 2016. Shoji continued to help the side remain at the top of the table for the next eleven matches. It wasn't until on 16 September 2016 when he scored his second goal of the season, in a 3–0 win against Júbilo Iwata. At some point around this month, he signed a contract with the club. Following the club's qualification to finish third place at the end of the J.League second stage, Shoji later helped the club win the league after playing both legs to beat Urawa Red Diamonds 2–2 on aggregate through away goal. Shoji played all the four matches in the FIFA Club World Cup, as he helped Kashima Antlers reached the final, only to lose 4–2 against Real Madrid. Despite losing in the final, both Shoji and Naomichi Ueda's centre-back partnership were praised by the media, both in and outside of Japan. Shoji also helped the club reach the Emperor's Cup Final by beating Kawasaki Frontale 2–1. At the end of the 2016 season, he went on to make forty–five appearances and scoring two times in all competitions. For his performance in the 2016 season, Shoji was named J.League Best XI.