On 5 December 2016, Gómez opened scoreboard on 12th minute, following assist of José Sosa at week 14 encounter against Kayserispor, ended 2–1 for Beşiktaş at Kadir Has Stadium, Kayseri. On 10 December 2015, Gómez scored the only goal of Beşiktaş against Sporting at Europa League Group Stage week 6 encounter ended 3–1 for Portuguese side at Estádio José Alvalade, where Beşiktaş eventually were eliminated from the competition. On 14 December 2015, Gómez scored first goal of Beşiktaş by a diving header in derby game against Galatasaray that ended 2–1 for Beşiktaş at Atatürk Olympic Stadium. At week 16, Gómez opened scoring tally of Beşiktaş while they were 2–0 down against Osmanlıspor, which eventually ended 3–2 in favour of Beşiktaş at Osmanlı Stadium in Ankara, on 21 December 2015. On 28 December 2015, Gómez scored 2nd goal of week 17 encounter against Konyaspor that ended 4–0 at Başakşehir Fatih Terim Stadium. Being top scorer 13 goals along with Samuel Eto'o, Gómez completed first half of the season with highest shooting accuracy, providing 29 shoots on target. He also scored 2 goals at UEFA Europa League until the end of 2015.
In Süper Lig week 20 game against Gaziantepspor, Gómez scored twice on 61st and 70th minutes when Beşiktaş achieved a comfortable 4–0 win on 7 February 2016. Scoring on 64th minute, Gómez had the only goal scored on week 22 game against Gençlerbirliği and secured the 1–0 win for Beşiktaş, on 26 February 2016. Gómez scored twice against Eskişehirspor at week 24 game on 7 March 2016, which ended 3–1 for Beşiktaş. His tally lead him to reach 19 Süper Lig goals and thus equilsed the "most scoring foreign player in single Süper Lig season" record of Beşiktaş, along with Pascal Nouma and Demba Ba.
Beşiktaş and Trabzonspor faced each other on rescheduled week 19 game on 14 March 2016, in which Gómez scored the first goal of the two, on 76th minute, finally ended 2–0 in favour of Beşiktaş. Gómez was the scorer of the first goal ever scored on newly built Vodafone Park, on 22nd minute of week 28 encounter against Bursaspor of 2015–16 season, ended 3–2 as well as the first ever win of the hosting side Beşiktaş at this stadium, on 11 April 2016. This was his 21st goal of 2015–16 season.
In May 2016, Gómez continued to produce goals. He scored once more at Istanbul derby versus Galatasaray at 76th minute which sealed the final score of 1–0 for Beşiktaş at Türk Telekom Stadium, on 8 May 2016 at week 32. 15 May 2016, at match week 33, scoring in fifth consecutive Süper Lig games, Gómez converted another strike and remaked his last Süper Lig goal of the season against Osmanlıspor on 48th minute, the latter of 3 goals scored by Beşiktaş as the score of 3–1. Thus, producing the 28th goal in all competitions, Gómez became the "most scoring foreign player across all competitions in single season", beating previous record of Demba Ba with 27 goals scored 2014–15 season.
Gómez scored total of 26 goals at 2015–16 Süper Lig season and became top scorer ahead of Samuel Eto'o and Hugo Rodallega. He completed the season with 28 goals in 41 games played in all competitions. On 20 July 2016, Gómez announced his farewell message via his Facebook account that he will not continue to play for Beşiktaş following a personally described "difficult decision" on a political basis, which was perceived as a reference to 2016 coup d'état attempt in country.
On 17 August 2016, Gómez returned to the Bundesliga to sign for VfL Wolfsburg. He scored his first goal for the club on 22 October, netting in a 3–1 defeat to Darmstadt 98. His goal was the 1,000th scored by Wolfsburg in the Bundesliga. On 2 April 2017, Gómez scored his first hat-trick for the club, netting three times in seven minutes as Wolfsburg came from 2–0 down to draw 3–3 with Bayer Leverkusen. His third on the night was his 150th goal scored in the Bundesliga. He ultimately scored 16 league goals for the season as Wolfsburg narrowly avoided relegation via the relegation play-offs. He finished the 2016–17 season with 18 goals in 37 appearances in all competitions.
On 21 June 2016, Gómez was selected to start in Germany's final Euro 2016 group match against Northern Ireland, scoring the winning goal in the 30th minute. On 26 June 2016, Gómez scored in the 43rd minute in Germany's Round of 16 3–0 win against Slovakia, becoming Germany's all-time leading scorer at the UEFA European Championship with five goals.