Pepperoni was a type of meat. It was often used as a topping on pizza.
While Enterprise was in a bad shape after a confrontation with the Xindi, T'Pol got a ration pack with pepperoni pizza. As she was a vegetarian, Commander Charles Tucker III suggested she pick off the pieces of pepperoni rather than eating them. (ENT: "The Forgotten")
In 1986 Dr. Gillian Taylor ordered two mushroom pizzas with pepperoni in a restaurant for time traveler James T. Kirk and herself. Star Trek IV: The Voyage Home
While suffering from the effects of crossing the transwarp threshold, Lieutenant Tom Paris stated that he was craving a piece of pepperoni pizza. (VOY: "Threshold")