It is understood Bulut was with a group of four, which included family members, who were involved in a verbal altercation with McDonald's staff who allegedly asked them all to leave.
Reports claimed the group was angered by the request and allegedly told the store manager that they should take the argument outside to the car park.
Police investigated the incident with Bulut - who was accompanied by Wanderers CEO John Tsatsimas at the Auburn police station late on Wednesday afternoon - only hours before his side took on, and defeated Melbourne City 3-2 at Pirtek Stadium.
It is understood Bulut was not directly involved in the verbal altercation but was identified as a Wanderers player.
He was charged with one count of intimidation and was granted conditional bail. He will appear in Burwood Local Court on 7 April.
Wanderers coach Tony Popovic explained he was made aware of the incident on Wednesday afternoon.
"He was stood down from the game due to that incident," Popovic said.
"Now it's with the club and the authorities and it's in their hands."
In a statement released late on Wednesday, the Wanderers said they would work with the police and FFA to resolve the matter.
The organising body gave its backing to the club over its handling of the incident.
"FFA has been informed by Western Sydney Wanderers of an incident involving Kerem Bulut and the subsequent action by NSW Police," an FFA spokesperson said.
"FFA supports the steps taken by the club in this matter and will await further advice from the club."
This is not the first time Bulut has caused headlines for the wrong reasons, with the the 23-year-old being charged with gang-related crimes in 2010.
He spent over four years playing in Europe before returning to Australia to join the Wanderers in January, and told The World Game recently he was moving on from his past indiscretions and focused on playing football and delivering on his potential.
Bulut scored two goals on debut for the Wanderers in their 4-3 loss in the Sydney derby on 28 February.