He started the 2016–17 season as the undisputed leader in BVB defence. On 15 September 2016, he netted the second goal in an away crashing 6–0 against Legia Warsaw on a Group Champions League match. On 4 January 2017 the German magazine ""kicker"" listed the Greek international as one of the best players in the German Bundesliga. The magazine paid a tribute to the best players currently playing in the German Bundesliga, separating them out into different categories. In the first category (World Class) no defenders were listed, however, Papastathopoulos was one of three defenders listed in the second category, International Class. The other two defenders included Mats Hummels of Bayern Munich and Jonathan Tah of Bayer Leverkusen.