Season the beef cubes generously with salt and black pepper.
Heat olive oil in a large skillet over medium-high heat. Add the beef cubes in batches and brown on all sides, about 4-5 minutes per batch. Transfer browned beef to the slow cooker.
In the same skillet, add diced bacon and cook until crisp, about 5 minutes. Using a slotted spoon, transfer bacon to the slow cooker with the beef, leaving the fat in the skillet.
Add diced onion to the skillet and sauté until softened, about 5 minutes. Add minced garlic and cook for 1 more minute.
Stir in tomato paste and cook for 2 minutes. Sprinkle flour over the mixture and stir to combine, cooking for another 2 minutes to remove raw flour taste.
Gradually pour in the red wine, scraping the bottom of the skillet to loosen browned bits. Bring to a simmer and cook for 5 minutes until slightly thickened.
Pour the wine mixture over the beef and bacon in the slow cooker. Add beef broth, bay leaf, and thyme sprigs. Stir gently to combine.
Add sliced carrots to the slow cooker. Cover and cook on low for 7 hours or on high for 4 hours, until beef is tender.
About 30 minutes before the end of cooking, melt butter in a large skillet over medium heat. Add pearl onions and mushrooms and sauté until golden and tender, about 8-10 minutes.
Stir the cooked mushrooms and pearl onions into the slow cooker. Continue cooking uncovered for the remaining 30 minutes to blend flavors and thicken the sauce slightly.
Remove bay leaf and thyme sprigs. Taste and adjust seasoning with salt and black pepper as needed.
Serve hot, garnished with chopped fresh parsley.