Pepperoni was a type of processed meat. It was often used as a topping on pizza.
While Enterprise was in a bad shape after a 2154 confrontation with the Xindi, T'Pol got a ration pack with pepperoni pizza. As she was a vegetarian, Commander Charles Tucker III suggested she could 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 in 2372, Lieutenant Tom Paris stated that he was craving a piece of pepperoni pizza with Kavarian olives. (VOY: "Threshold")