Heat 2 tablespoons olive oil in a large skillet over high heat and cook beef, onion, and garlic until meat is browned on all sides and onions are soft, 6 to 8 minutes. Add tomatoes, nutmeg, cinnamon stick, bay leaves, rosemary, salt and a good pinch of black pepper. Cook over medium heat, stirring occasionally, until ingredients blend, about 3 minutes. Add wine and vinegar and stir to combine.
Turn slow cooker to Low setting. Pour beef mixture into slow cooker and stir in ketchup.
Cook on Low until beef is tender, 6 to 8 hours.
Meanwhile, heat remaining olive oil in a skillet and cook shallots until soft, 3 to 4 minutes. Add cooked shallots to stew for the last 1 to 2 hours of cooking.
Remove and discard cinnamon stick, bay leaves, and rosemary sprig before serving.