Preheat the oven to 325°F (160°C).
Pat the beef cubes dry with paper towels. Season them with 1 teaspoon salt and 1/2 teaspoon black pepper.
In a large Dutch oven or heavy oven-safe pot, heat 2 tablespoons olive oil over medium-high heat.
Add the diced bacon and cook until crisp, about 5 minutes. Remove the 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, about 5 minutes per batch. Remove browned beef and set aside.
Add the sliced 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 onions and garlic, stirring constantly to cook the flour for 2 minutes.
Gradually pour in the red wine, scraping the bottom of the pot to release browned bits.
Add the beef broth and bouquet garni, then return the beef and bacon to the pot. Bring to a simmer.
Cover the pot with a lid and transfer it to the preheated oven. Cook for 2 hours.
While the beef cooks, heat 1 tablespoon olive oil and 1 tablespoon butter in a skillet over medium heat.
Add the pearl onions and carrots, sautéing until they begin to soften and brown, about 10 minutes. Remove and set aside.
In the same skillet, add the remaining 1 tablespoon butter and sauté the mushrooms until browned, about 8 minutes. Remove and set aside.
After 2 hours, remove the pot from the oven and add the sautéed pearl onions, carrots, and mushrooms.
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.
Taste and adjust seasoning with salt and black pepper as needed.
Sprinkle chopped fresh parsley over the stew before serving.