Cut off the tops of the peppers and scrape out the ribs and seeds. Dice the onion and measure a ¼ cup.
In a bowl, combine the quinoa, beans, tomato sauce, spices, onion, and ½ cup of the cheese. Fill each pepper with the mixture.
Pour ¼ cup water into the bottom of a slow cooker. Place the peppers in the water. Cover and cook on low for about 5 hours or on high for about 2 hours or until quinoa is tender.
Remove the lid, distribute the remaining cheese (¼ cup) on top of the peppers, and cover again until the cheese is melted.