Preheat the oven to 325°F (160°C).
Pat the beef cubes dry with paper towels and season generously with salt and black pepper.
In a large Dutch oven or heavy-bottomed pot, heat 2 tablespoons of olive oil over medium-high heat.
Add the diced bacon and cook until crisp. Remove 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 without overcrowding. Remove browned beef and set aside.
Add the chopped onion to the pot and sauté 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.
Return the beef and bacon to the pot and sprinkle the flour over the meat. Stir to coat and cook for 2 minutes to remove the raw flour taste.
Slowly pour in the red wine, scraping the bottom of the pot to release browned bits.
Add the beef broth and bouquet garni. Bring to a simmer.
Cover the pot and transfer to the preheated oven. Cook for 2 1/2 to 3 hours, or until the beef is very tender.
While the beef cooks, prepare the pearl onions: bring a small pot of water to a boil, add the pearl onions, and blanch for 2 minutes. Drain and peel the onions.
In a skillet, heat 1 tablespoon olive oil and 1 tablespoon butter over medium heat. Add the pearl onions and cook until golden and tender, about 10 minutes. Set aside.
In the same skillet, add the remaining 1 tablespoon butter and sauté the mushrooms until browned and their moisture evaporates, about 8 minutes. Set aside.
When the beef is tender, remove the pot from the oven and place over medium heat on the stove.
Remove the bouquet garni and discard.
Add the cooked pearl onions and mushrooms to the stew. Simmer uncovered for 15 minutes to blend flavors and thicken the sauce slightly. Adjust seasoning with salt and pepper as needed.
Sprinkle chopped fresh parsley over the stew before serving.