Bring water and barley to a boil in a pot over high heat. Cover and reduce heat to a simmer. Let simmer until most of the water is absorbed, about 30 minutes.
Meanwhile, place a steamer insert into a saucepan and fill with water to just below the bottom of the steamer. Bring water to a boil. Add bell peppers, cover, and steam until just tender, about 5 minutes. Rinse peppers under cold water. Cut off the tops and reserve to cover filled peppers.
Remove barley from heat and keep covered for 5 to 10 more minutes.
Preheat the oven to 350 degrees F (175 degrees C).
Transfer barley to a large bowl and mix in refried beans. Sprinkle in black pepper and mix well. Stuff the peppers with the barley and refried beans mixture. Arrange peppers in a small baking dish and sprinkle vegan cheese over the filling. Cover with the reserved tops.
Bake in the preheated oven until centers are very hot, about 30 minutes. Let cool for at least 5 minutes before serving.
