Heat the olive oil in a large skillet over medium-high heat. Working in batches, brown the beef cubes on all sides, about 3-4 minutes per batch. Transfer the browned beef to your slow cooker.
In the same skillet, sauté the onion and jalapeño until softened, about 5 minutes. Add the garlic and cook for another minute. Transfer to the slow cooker.
Add the chopped chipotle peppers with adobo sauce, crushed tomatoes, pinto beans, kidney beans, beef broth, chili powder, cumin, cocoa powder, oregano, salt, and pepper to the slow cooker. Stir everything together really well.
Cover and cook on LOW for 8-10 hours or on HIGH for 5-6 hours, until the beef is incredibly tender and shreds easily with a fork.
Give it a good stir before serving, breaking up any larger pieces of beef. Taste and adjust seasoning if needed—you might want to add more adobo sauce if you like it spicier!
Serve hot with dollops of sour cream, shredded Monterey Jack cheese, and sliced green onions on top.