Place a large heavy-bottomed pot (such as a Dutch oven) over medium-high heat.
Heat the olive oil for a minute, and then add the onions, celery, and carrots.
Sauté the vegetables for 3-5 minutes, until the onions are becoming translucent. Add the garlic, and sauté another 2-3 minutes.
Add the cubed butternut squash, and red peppers, and stir to combine. Continue to cook the vegetables for another 5 minutes, stirring frequently.
Add the diced chipotle pepper, cumin, chili powder, oregano, and smoked paprika. Stir to combine well.
Add the kidney beans, black beans, crushed tomatoes, quinoa, and vegetable broth. Stir.
Allow the chili to come to a boil, and then reduce the heat to medium-low, cover, and simmer for 30 minutes until the quinoa is cooked and the vegetables are tender.