**Prepare the Beef:** Season the beef cubes with salt and pepper. Heat the Dutch oven over medium heat and cook the bacon until crispy. Remove the bacon and set aside.
**Sear the Beef:** In the same pot, add the beef cubes in batches and sear them on all sides until browned. Remove and set aside.
**Sauté Vegetables:** Add olive oil to the pot. Sauté the onions and carrots until softened, about 5 minutes. Add garlic and cook for another minute.
**Deglaze the Pot:** Stir in tomato paste and cook for 2 minutes. Sprinkle in the flour and mix well. Gradually pour in the wine, scraping the bottom to release any browned bits.
**Simmer the Stew:** Return the beef and bacon to the pot. Add the beef stock, thyme, bay leaves, and a pinch of salt and pepper. Bring to a boil, then reduce the heat to low. Cover and simmer for 2.5–3 hours, stirring occasionally.
**Prepare the Garnish:** In a skillet, melt butter and sauté the mushrooms until golden brown. Add the pearl onions and cook until tender.
**Combine and Serve:** Once the stew is cooked, stir in the mushrooms and pearl onions. Discard the bay leaves. Serve hot, garnished with fresh parsley.