After having only earned seven caps and most of them as a substitute during the first half of the 2014–15 season, Petersen was loaned to SC Freiburg for the second leg of the campaign.
On 31 January 2015, in his league debut versus Eintracht Frankfurt, he scored a hat-trick, despite just coming on as a substitute for the second half, ultimately helping his team turning a 0–1 deficit into a 4–1 victory.
He subsequently made appearances on matchdays 19 and 20.
Christian Streich, Freiburg's head coach, stated that Petersen was "an option for the squad."
He finished the 2014–15 season by scoring nine goals in 12 matches for Freiburg.

On 28 June 2015, Petersen joined newly relegated Freiburg on a permanent deal, for an undisclosed fee.
On 27 July 2015, he marked his season debut by scoring a hat-trick in a 6–3 victory over 1.
FC Nürnberg.
On 9 August 2015, he continued his good form by scoring his second hat-trick in three games, in a 5–0 win at fifth-tier side HSV Barmbek-Uhlenhorst in the first round of the DFB-Pokal.
He finished the 2015–16 season by scoring 25 goals in 34 matches.

Petersen made his 100th top flight appearance on 29 October 2016 by coming on in the second half of the 3–1 away win against his former side Werder Bremen.
He scored his first Bundesliga hat-trick later on 10 December 2017, including two penalties in the injury time, in the 4–3 win at 1.
FC Köln.

In the 2017–18 season, Petersen was the top scoring German in the Bundesliga with 15 goals, finishing second to only Robert Lewandowski of Bayern Munich.
On 19 January 2019, he scored his 38th league goal for Freiburg, breaking the club's all-time Bundesliga goalscoring record previously held by Papiss Cissé.
After having only earned seven caps and most of them as a substitute during the first half of the 2014–15 season, Petersen was loaned to SC Freiburg for the second leg of the campaign. On 31 January 2015, in his league debut versus Eintracht Frankfurt, he scored a hat-trick, despite just coming on as a substitute for the second half, ultimately helping his team turning a 0–1 deficit into a 4–1 victory. He subsequently made appearances on matchdays 19 and 20. Christian Streich, Freiburg's head coach, stated that Petersen was "an option for the squad." He finished the 2014–15 season by scoring nine goals in 12 matches for Freiburg.
On 28 June 2015, Petersen joined newly relegated Freiburg on a permanent deal, for an undisclosed fee. On 27 July 2015, he marked his season debut by scoring a hat-trick in a 6–3 victory over 1. FC Nürnberg. On 9 August 2015, he continued his good form by scoring his second hat-trick in three games, in a 5–0 win at fifth-tier side HSV Barmbek-Uhlenhorst in the first round of the DFB-Pokal. He finished the 2015–16 season by scoring 25 goals in 34 matches.
Petersen made his 100th top flight appearance on 29 October 2016 by coming on in the second half of the 3–1 away win against his former side Werder Bremen. He scored his first Bundesliga hat-trick later on 10 December 2017, including two penalties in the injury time, in the 4–3 win at 1. FC Köln.
In the 2017–18 season, Petersen was the top scoring German in the Bundesliga with 15 goals, finishing second to only Robert Lewandowski of Bayern Munich. On 19 January 2019, he scored his 38th league goal for Freiburg, breaking the club's all-time Bundesliga goalscoring record previously held by Papiss Cissé.
Nils Petersen