In the 2015/2016 season Koukalová put in strong performances: at the fifth round of the World Cup on 4 January 2016, even two missed targets did not prevent her from making the podium. Gabriela showed good consistency, finishing no lower than 11th place during the season, and continued to lead the World Cup standings. In the 12.5 km mass start on 16 January 2016 she won and got her tenth victory in the Biathlon World Cup. She also helped to win a silver for the team in the 4x6 km relay on 24 January 2016, and took a third place in the mass start in Canada on 6 February 2016. In the US at Presque Isle on 11 February 2016 in sprint she got the best result showing a perfect accuracy and an excellent performance. The following days brought two gold medals in the 10 km pursuit and 4x6 km relay. Despite some poorer results in Norway, Koukalová took a better result in the sprint in Khanty-Mansiysk in Russia on 17 March 2016 clinching her the small Crystal Globe in the sprint with a total of 413 points. On the next day in the pursuit she got a fourth place, but with very good level both in speed and shooting. She also took a second small Crystal Globe in the mass start with 241 points. She led the standings in the 2015/2016 World Cup from start to finish, and won the overall Crystal Globe on 20 March 2016 with a final score of 1074 points.
The 2016/2017 season started in Östersund, Sweden on 27 November 2016, where she and her teammates took 7th place in the mixed relay. The 15 km race on 30 November 2016 brought a 17th place, but later on, on 3 December 2016, she took third place in the 7.5 km sprint, and the next day she showed even better results - winning the pursuit, showing an excellent performance both in skiing and shooting. The next medal (first place) was taken in a mass start race on December 18, 2016.