Season the beef with salt and pepper. Heat oil in a large, heavy-bottomed pot over medium-high heat. Add the beef in one layer and cook until deeply browned on all sides, about 15-18 minutes. Transfer the beef to a plate, leaving the fat behind.
Add onions and garlic to the pot, season with salt and pepper, and cook until softened and translucent, about 3–5 minutes. Add tomato paste and cook until it turns brick red, about 2–3 minutes. Add cumin, paprika, and chili flake, and cook for a minute to toast the spices.
Add beer, scraping up the caramelized bits at the bottom of the pot, followed by crushed tomatoes, beans, 6 cups of water, and the beef plus any juices. Season with salt and pepper and bring to a strong simmer.
Reduce the heat to medium-low and partially cover the pot. Cook, checking and stirring occasionally, until the pot has thickened and the beef and beans are tender, about 3–3 ½ hours.
Remove from heat and encourage the hunks of beef to break down into smaller bits by pressing them against the side of the pot. Stir to distribute the meat and season again with salt, pepper, and crushed red pepper flakes if desired.
To serve, set out all the toppings and encourage guests to customize their bowls.
