In his first professional season, he featured in 26 league games and scored 4 goals as Freiburg won the 2. Bundesliga and promoted after a defeat of VfL Osnabrück. On 9 June 2009, Toprak suffered from a karting accident, causing him to miss the first half of the 2009–10 season but he recovered, scoring a goal against Hamburger SV on the 65th minute. Toprak played 24 league games during the 2010–11 season.
On 9 June 2009, Toprak was involved in a karting accident, in which he suffered severe burns and had to be treated in a special clinic. He was able to resume training after only four months.