Stander captained Munster in their opening fixture of the 2015–16 Pro12 against Benetton on 5 September 2015, scoring two tries and earning the Man-of-the-Match award in the 18–13 win for Munster. He came off the bench against Ospreys on 13 September 2015, scoring a try that leveled the scores and allowed Ian Keatley to kick the conversion that won the match for Munster. On 30 October 2015, Stander captained Munster in their 32–38 win against provincial rivals Ulster. On 4 November 2015, it was announced that, in the absence of regular captain Peter O'Mahony, Stander would captain Munster during the pool stage of the 2015–16 European Rugby Champions Cup. He started the opening pool game of the tournament against Benetton on 14 November 2015, scoring a try and earning the Man-of-the-Match award in Munster's 32–7 win.