Pat the beef dry with paper towels so it browns properly instead of steaming. Season generously with salt and pepper. In a large Dutch oven, cook the diced bacon until crispy and golden, then remove it while leaving the flavorful fat behind.
Working in batches, sear the beef cubes in the bacon fat and olive oil. Avoid overcrowding the pot, as this prevents proper browning. Each piece should develop a deep brown crust for maximum flavor.
Add chopped onions and carrots to the same pot and cook until slightly softened. Stir in the garlic and cook briefly until fragrant. This builds the aromatic base of the stew.
Stir in tomato paste and flour, coating the vegetables evenly. Pour in the red wine while scraping the bottom of the pot to release browned bits. Add beef stock, thyme, bay leaves, bacon, and beef.
Bring to a gentle simmer, then cover and cook in a preheated 325°F (165°C) oven for about 2½ hours. The beef should be fork-tender and the sauce thickened.
While the stew cooks, sauté mushrooms and pearl onions until golden. Add them during the final 30 minutes so they keep their texture.
Remove bay leaves and thyme stems. Let the stew rest for 10 minutes before serving. Garnish with fresh parsley.