Some people who shook hands with the campaign leader yesterday at Glasgow Central Mosque were rebuked by others, who shouted that the former Labour Cabinet minister had "blood on his hands" over Britain's invasion of Iraq.
It came as accusations of intimidation flew from senior Labour figures during their final weeks of campaigning ahead of next month's poll.
Jim Murphy, the party's international development spokesman, said he had suspended his 100 Towns In 100 Days tour of Scotland, which has seen him take to a soapbox to get his anti-independence message across, after he was pelted with an egg in Kirkcaldy town centre, Fife, on Thursday.
The East Renfrewshire MP later said he would restart the tour after receiving advice from police and pledges by the Yes campaign to "call off the attack dogs".
However, the Yes campaign accused the MP of negativity in an attempt to scare people away from the debate as its leaders condemned any kind of abusive or offensive and dangerous behaviour.
It also said that First Minister Alex Salmond had called in police after being chased in his official car by a motorist waving a No sign.
A Yes spokesman said: "For the most part, the independence debate has been conducted in a responsible, peaceful and enthusiastic manner with only a very small minority on both sides behaving badly."
In an incident, on Thursday, shadow foreign secretary Douglas Alexander was accused by a man on a Radio Scotland phone-in show of scaremongering over independence and of being a "f****** liar".
The incidents involving Mr Darling saw mosque visitors split over his attendance at Friday prayers, with some shaking hands and posing for "selfie" photographs while others looked on in disapproval.
One heckler tackled Mr Darling over his views on the Israel-Gaza conflict, and on the then Labour Government's military intervention in Iraq in 2003 under Tony Blair.
Abdull Oun, 27, said: "I was an undecided voter and my question was very simple: If I vote No, what are your views on the conflict, what are your views on military intervention?
"He didn't answer, he just walked away. He just waved his hand, I was basically dismissed. He demands answers from Alex Salmond on issues like currency, but he couldn't give me answers."
Mr Oun, who works for a non-profit making organisation in Glasgow, added: "He came here to meet and greet Muslims, but it is a publicity stunt and it has failed."
Better Together spokesman David Whitton, who was with Mr Darling at the mosque, said: "The chap had shouted across because he wanted to speak to Alistair, but the thing was pretty crowded and the guy couldn't get close to Alistair, so he shouted across.
"The Muslim elders lost the plot a little bit and started shouting at him (Mr Oun).
"Somebody apparently tweeted that Alistair had run off. He didn't do any of that, he went into the meeting with the committee members of the mosque. We were on a tight schedule so we had to get him away to do that.
"The committee were asking the same questions as everyone else to do with a currency union, what happens to jobs, etc."
Better Together staff later invited Mr Oun and another man in for a private conversation with Mr Darling and Scottish Labour deputy leader Anas Sarwar.
"The men said they just wanted to ask Alistair some questions - that's what we were there for so that's what we did," the spokesman said.
"The two of them were shown into the room, we did the television interviews and then Anas and Alistair went to talk to them, they shook hands and they left."
Mr Whitton said he did not hear hecklers shouting Mr Darling has "blood on his hands".
He added: "I would not be surprised in a mosque if there was split views on whether or not Alistair should be there.
"I think there would probably be split views if Alex Salmond was there.
"The Muslim community is just like every other section of the Scottish community, they are split between those who vote Yes and those who want to vote No."