Chop the onion, garlic, and jalapeño into large chunks. Place in a food processor and pulse until everything is minced. Drain any liquid that may have formed.
Heat a stockpot over medium heat. Add olive oil and onion mixture. Cook until onions are fragrant and transparent, about 5 to 6 minutes.
Stir in spices and about half a teaspoon of sea salt, cooking for 1 to 2 minutes or until you can smell the spices.
Add in the crushed tomatoes, bittersweet chocolate, and 3 cups of the vegetable broth. Bring to a boil, reduce to a simmer, cover, and let cook for 5 minutes.
After 10 minutes, stir in the pecan meal and beans. Cover and cook for another 10 to 15 minutes. Taste and adjust the salt/seasoning.
Add more vegetable broth if a thinner consistency is desired.
Divide into four bowls and top with your desired toppings.