Heat a large skillet over medium heat. Add the oil and the onion and sauté until translucent, 3-5 minutes. Add the chicken, season with salt and pepper, and cook until golden brown, about 5 minutes. Add the garlic and continue to cook for 2 minutes. Remove from heat and transfer the mixture to a medium bowl.
Mix together all the burrito spice mix ingredients, and then add the spice mix to the chicken mixture. Add the diced tomatoes and stir until completely combined.
Preheat the oven to 350°F (180°C). Grease a 12-cup muffin tin.
Place the 6 tortillas on top of each other. Cut them into a square shape, and then cut the square into quarters.
In the prepared muffin tin, place a tortilla square in each cup and push down. Push another layer of tortilla on top of each in a star formation. Spread some refried beans on the bottom of each tortilla cup, then add the cooked rice, and then the chicken mixture. Top each cup with cheddar cheese. Bake for 15 minutes, until the tortillas are brown and crispy and the cheese is melted.
Serve with sour cream, guacamole, salsa, and cilantro on the side.