Preheat the oven to 325°F (163°C).
Pat the beef cubes dry with paper towels and season them generously with salt and black pepper.
In a large Dutch oven or heavy-bottomed ovenproof pot, heat 2 tablespoons of olive oil over medium-high heat.
Add the diced bacon and cook until crisp. Remove bacon with a slotted spoon and set aside, leaving the fat in the pot.
Add the beef cubes in batches to the pot, browning them on all sides. Do not overcrowd the pot. Remove browned beef and set aside.
Add the chopped onion to the pot and cook until softened, about 5 minutes.
Add the minced garlic and cook for 1 minute until fragrant.
Stir in the tomato paste and cook for 2 minutes.
Sprinkle the flour over the vegetables and stir well to coat. Cook for 2 minutes to remove the raw flour taste.
Gradually pour in the red wine, scraping the bottom of the pot to loosen any browned bits.
Add the beef broth and bouquet garni. Return the browned beef and bacon to the pot.
Bring to a simmer, then cover the pot with a lid and transfer it to the preheated oven.
Cook for 2 hours, stirring occasionally.
While the stew cooks, heat 1 tablespoon of olive oil and 1 tablespoon of butter in a skillet over medium heat.
Add the pearl onions and cook until they are golden and tender, about 10 minutes. Set aside.
In the same skillet, add the remaining 1 tablespoon butter and sauté the mushrooms until browned, about 8 minutes. Set aside.
After 2 hours, add the sliced carrots, cooked pearl onions, and sautéed mushrooms to the stew.
Return the pot to the oven and cook uncovered for an additional 1 hour, until the beef is very tender and the sauce has thickened.
Remove the bouquet garni and discard.
Adjust seasoning with salt and pepper to taste.
Serve hot, garnished with chopped fresh parsley.