Heat the oil in a heavy soup pot over medium heat. Add the onions to the pot and sauté until translucent and softened, about 4-5 minutes. Add the garlic, cumin, chili powder, coriander, and cocoa to the pot and stir. Once the garlic is fragrant, about 30 seconds, add the squash, quinoa, and some salt and pepper. Stir to coat everything in the cocoa and spices.
Once everything is starting to dry up/stick, add the adobo sauce and vegetable stock to the pot and stir, scraping the bottom of the pot to get any golden brown bits. Add the crushed tomatoes, pinto beans, black beans, poblano pepper, and a bit more salt and pepper to the pot. Stir to combine. Bring the smoky squash chili to a boil.
Once boiling, lower the heat to a simmer and place a lid on top of the pot. Let the chili simmer until the squash is soft all the way through, about 25-28 minutes. Check the smoky squash chili for seasoning one more time and adjust if necessary. Serve the chili hot with chopped cilantro on top.