Place the chopped bacon in a large skillet over medium heat and cook until crisp. Remove the bacon with a slotted spoon and set it aside, leaving the drippings in the pan.
Add the beef cubes to the skillet in batches. Brown on all sides, then transfer the beef to the slow cooker.
Add the diced onion and minced garlic to the same skillet. Cook for 3 minutes until the onion softens, then stir in the tomato paste and flour. Cook for 1 minute more.
Pour the red wine into the skillet and scrape up any browned bits. Let it simmer for 2 minutes, then transfer everything to the slow cooker.
Add the mushrooms, beef broth, thyme, bay leaves, cooked bacon, salt, and pepper to the slow cooker. Stir to combine.
Cover and cook on low for 8 hours or on high for 5 hours until the beef is fork-tender. Remove the bay leaves before serving.