It was alleged the striker and his friends lobbed the £1.99 chocolate treat while shouting abuse at customers in the Gorgie Road branch.
Bosses at the McDonald’s outlet said he had been barred for “unacceptable” behaviour and that he would be informed of the decision by letter.
But a source close to the 19-year-old – who has scored 12 goals this season – denied Cummings was directly involved in the melee and CCTV footage would prove his innocence.
It is understood Cummings had been “upset” by the allegations.
“He was in the wrong place at the wrong time and got caught up in something that wasn’t his doing,” said a source.
“Thankfully, he has the full support of the club and his manager, Alan Stubbs, and as ever he’s working hard to get back in the team for their game against Alloa on Saturday.
“He just wants to put this behind him and get on with scoring goals for Hibs.”
An 18-year-old man, who claimed to be a friend of Mr Cummings, said the fast food giant was trying to rub the footballer’s “name in the dirt”.
He said: “Jason is innocent. It was actually not Jason that threw the muffin. It was our mate.
“He just chucked a chocolate muffin at one of the managers for no reason at all.
“We were having some good banter and they first laughed but then someone clicked the panic button and told us to leave.
“We’ve all been banned from McDonald’s. McDonald’s tried to get to Jason and rub his name in the dirt.”
Police have confirmed they are investigating a disturbance on Gorgie Park Road at around 7.51am on February 15.
Mr Cummings did not play in his side’s 3-0 win over Dumbarton at the weekend amid rumours he had been disciplined by team bosses but scored for the under-20s against Kilmarnock.
The striker took to Twitter yesterday to tell his 6500 followers: “The Muffin Man – wow just have to laugh.”
A McDonald’s spokeswoman said: “Following behaviour deemed to be unacceptable, we are in the process of writing to this individual, informing him of our decision to ban him from the Gorgie Road restaurant. He will receive a banning letter for antisocial behaviour.
“Our first priority is to ensure that our restaurants are a safe and welcoming environment for our customers and employees, so we take antisocial behaviour very seriously. Another member of the group has also been sent a letter banning them from the restaurant following their behaviour and the CCTV footage has been shared with the police who are investigating further.”
Hibs declined to comment.