Revive founder and owner Jeremy Dixon said the charity did "amazing" work, often under difficult circumstances, however, he had been surprised by its response.
"We were absolutely flabbergasted."
He told the Herald he could "see why they made this call" because "pies and cakes and things like that do taste better if you aren't used to eating healthy food".
However, he added: "I feel these people in need should be given the best food options, not the ones they just want".
The menu at Revive featured salads, curries, soups, and hot meals - such as frittatas.
"It's all healthy food. Vegetarian. We don't use white flour or processed sugars. If you eat healthy food your brain works better, you can make better decisions."
It was the first time in five years the offer of free meals had been rejected, Dixon said.
Auckland City Mission's Chris Farrelly said he had been surprised to find out a staff member had asked Revive to stop donating.
"There's a complete shock and horror here about this. We are incredibly accepting and grateful of vegetarian food."
The Mission was investigating who had called Revive because none of the team leaders who usually communicated with suppliers had been involved, Farrelly told the Herald.
He said when the call was placed in August the Mission's chiller was broken, so donated food that needed to be kept cool could not be stored on the premises overnight.
Farelly suspected the call had been made following a miscommunication between staff members about food storage. "That's all we can put it down to."
Farrelly said he was saddened by what had happened and the Auckland City Mission would "absolutely" want to reinstate its partnership with Revive if possible.
"The homeless should have the best of everything, including healthy food options," he said.