Bring the quinoa and water to a boil in a saucepan over high heat. Reduce heat to medium-low, cover, and simmer until the quinoa is tender, 20 to 25 minutes.
Preheat oven to 350 degrees F (175 degrees C). Lightly grease a small baking dish. Halve the red peppers lengthwise. Remove the seeds and ribs, but leave the stem intact so the pepper bowls hold their shape; place cut-side-up into the prepared baking dish.
Toss the chopped apple with the lime juice, olive oil, garlic, parsley, mint, tomatoes, and green onions. Fold in the quinoa, and season to taste with salt and pepper. Fill the cut peppers with this mixture, and fill the baking dish with about 1/4 inch of water.
Bake in preheated oven until the peppers are tender, and the quinoa is hot, about 20 minutes.