He also sampled blue cheese and Northern Irish butter on crackers but turned down a taste of some smoked salmon as he chatted with the producers, accompanied by The Secret star James Nesbitt, who is from Ballymena.
Charles sniffed the whiskey and toasted Nesbitt and his hosts before he drank it all in one go and remarked: "It's very good, it goes straight up the nose."
Shane Braniffe, managing director of Echlinville Distillery in Kircubbin, Co Down, said the senior royal seemed to love his taste of the drink, which is on sale at the department store for £46.75.
He said: "He said he might have to change his allegiance from being a Bushmills man to a Dunville man.
"It was lovely to see him drink it. If he left half a glass that wouldn't have looked good but he drank it all so I'm glad he approved. It wasn't just politeness."
Charles, who walked over to the department store from nearby Clarence House carrying an umbrella, also inspected Irish Lumpers potatoes from Glen's of Antrim and some Abernethy Butter, a Stilton from Mike's Fancy Cheese, Glenarm organic salmon and Glenarm Himalayan salt-aged beef from Hannan Meats as part of Fortum & Mason's pop-up "year of food in Northern Ireland celebration".
Nesbitt said: "This is two weeks celebrating ordinary craftsman doing extraordinary things.
"To have the endorsement of Prince Charles is very important.
"As Northern Ireland continues to emerge we are trying to spread the goodness of the place.
"It's a perfect fit because of the knowledge he has about the process of farming organic produce.
"He seemed to be a big fan of the butter and the whiskey."
Charles also paid a visit to a stand displaying food and drink from his Highgrove Estate, which is on sale at the store.