Glasgow Central Mosque visitors were split over Mr Darling's attendance at Friday prayers, with some shaking hands and posing for "selfie" photographs while others looked on in disapproval.
Those shaking hands with Mr Darling are understood to have been rebuked by other mosque visitors, who shouted that he has "blood on his hands".
One heckler tackled Mr Darling over his views on the Israel-Gaza conflict, and on the Labour government's military intervention in Iraq 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 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 that Mr Darling has "blood on his hands".
He added: "I wouldn't 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."