On 9 January 2016, Botha ruptured his anterior cruciate ligament during Munster's match against Stade Français. The injury ruled him out for the foreseeable future. In May 2016, it was announced that Botha would leave Munster at the end of the 2015–16 season.
Botha suffered a severe knee injury on January 9, 2016, during Munster's game against Stade Français, forcing him to miss the rest of the season. Later in May 2016, it was announced that Botha would be leaving Munster at the end of the 2015–16 season.