Halstenberg signed a three-year contract with FC St. Pauli as a free agent, after his contract had expired with Borussia Dortmund at the end of the 2012–13 Bundesliga campaign.

Halstenberg made his FC St. Pauli debut in the opening game of the season, starting the whole game, in a 1–0 win over TSV 1860 Munich.
Since making his FC St. Pauli debut, he quickly established himself in the starting eleven, where he faced competition from another left–back position player, Sebastian Schachten.
He continued to start in the left–back position until Schachten's return in December 2013 and found himself, coming on as a substitute on two occasions and at one point, played in the left–midfield position.
It wasn't until on 23 February 2014 when Halstenberg scored his first goal for the club, scoring from a direct free kick, in a 2–1 win over Dynamo Dresden.
In a follow up match against Union Berlin, he played a vital role when he set up two goals, as FC St. Pauli won 2–1.
Halstenberg then set up another two goals, setting up the first and second goal, as FC St. Pauli beat SV Sandhausen 3–2 on 5 April 2014.
Towards the end of the 2013–14 season, he then began to play in the midfield positions following Schachten regaining his left–back position.
At the end of the 2013–14 season, Halstenberg went on to make thirty–two appearances and scoring once in all competitions.

In the 2014–15 season, Halstenberg, however, suffered an injuries that saw him missed the start of the season.
After returning to the reserve team from injuries, he made his first appearance of the season, starting the whole game, in a 4–1 loss against RB Leipzig.
In a follow–up match against 1.
FC Kaiserslautern, Halstenberg scored his first goal of the season, in a 3–1 loss.
Since returning to the first team, he regained his first team place in the left–back position, competing with Daniel Buballa throughout the season.
Halsternberg later two more goals later in the 2014–15 season against 1.
FC Kaiserslautern and VfL Bochum.
Despite being sidelined for one more game later in the 2014–15 season, he went on to make twenty–two appearances and scoring two times in all competitions.

Ahead of the 2015–16 season, Halstenberg was linked with a move away from the club, with his hometown club, Hannover 96 interested.
Hastlenberg, himself, stated he wanted to leave the club, describing it as the next step.
Despite, Halstenberg continued to regain his first team place.
He scored his first goal of the season, in a 2–1 win over Karlsruher SC on 2 August 2015.
This was followed up by scoring his second goal of the season, in a 3–2 win over Greuther Fürth.
However, he suffered an injury once again that saw him sidelined throughout August.
By the time of his departure, Halstenberg made three appearances and scoring once for the side.
Halstenberg signed a three-year contract with FC St. Pauli as a free agent, after his contract had expired with Borussia Dortmund at the end of the 2012–13 Bundesliga campaign.
Halstenberg made his FC St. Pauli debut in the opening game of the season, starting the whole game, in a 1–0 win over TSV 1860 Munich. Since making his FC St. Pauli debut, he quickly established himself in the starting eleven, where he faced competition from another left–back position player, Sebastian Schachten. He continued to start in the left–back position until Schachten's return in December 2013 and found himself, coming on as a substitute on two occasions and at one point, played in the left–midfield position. It wasn't until on 23 February 2014 when Halstenberg scored his first goal for the club, scoring from a direct free kick, in a 2–1 win over Dynamo Dresden. In a follow up match against Union Berlin, he played a vital role when he set up two goals, as FC St. Pauli won 2–1. Halstenberg then set up another two goals, setting up the first and second goal, as FC St. Pauli beat SV Sandhausen 3–2 on 5 April 2014. Towards the end of the 2013–14 season, he then began to play in the midfield positions following Schachten regaining his left–back position. At the end of the 2013–14 season, Halstenberg went on to make thirty–two appearances and scoring once in all competitions.
In the 2014–15 season, Halstenberg, however, suffered an injuries that saw him missed the start of the season. After returning to the reserve team from injuries, he made his first appearance of the season, starting the whole game, in a 4–1 loss against RB Leipzig. In a follow–up match against 1. FC Kaiserslautern, Halstenberg scored his first goal of the season, in a 3–1 loss. Since returning to the first team, he regained his first team place in the left–back position, competing with Daniel Buballa throughout the season. Halsternberg later two more goals later in the 2014–15 season against 1. FC Kaiserslautern and VfL Bochum. Despite being sidelined for one more game later in the 2014–15 season, he went on to make twenty–two appearances and scoring two times in all competitions.
Ahead of the 2015–16 season, Halstenberg was linked with a move away from the club, with his hometown club, Hannover 96 interested. Hastlenberg, himself, stated he wanted to leave the club, describing it as the next step. Despite, Halstenberg continued to regain his first team place. He scored his first goal of the season, in a 2–1 win over Karlsruher SC on 2 August 2015. This was followed up by scoring his second goal of the season, in a 3–2 win over Greuther Fürth. However, he suffered an injury once again that saw him sidelined throughout August. By the time of his departure, Halstenberg made three appearances and scoring once for the side.
Marcel Halstenberg