Place the chopped bacon in a skillet over medium heat. Cook until crisp, then transfer it to the slow cooker with a slotted spoon.
Add the beef cubes to the same skillet. Brown on all sides for about 5 minutes, then move the beef to the slow cooker.
Sprinkle the flour over the beef and bacon in the slow cooker. Stir to coat evenly.
Add the pearl onions, sliced carrots, halved mushrooms, minced garlic, tomato paste, dried thyme, bay leaf, salt, and black pepper.
Pour in the red wine and beef broth. Stir everything together until the tomato paste dissolves.
Cover and cook on low for 8 hours. Remove the bay leaf before serving.