Heat the olive oil in a large heavy-bottomed pot over medium heat until shimmering.
Add the diced onion and bell pepper, sautéing until they are soft and translucent.
Stir in the minced garlic and cook for 60 seconds until the aroma fills the kitchen.
Add the smoked paprika, chili powder, cumin, sea salt, and black pepper, stirring to toast the spices for one minute.
Pour in the black beans, kidney beans, pinto beans, tomato puree, and vegetable broth.
Bring the mixture to a gentle boil, then reduce the heat to low and simmer for 20 minutes to meld the flavors.
Stir in the nutritional yeast until fully incorporated to add a savory, cheese-like depth to the sauce.
Serve hot in bowls, topped with a generous dollop of Greek yogurt and a sprinkle of fresh cilantro.