Set the oven rack to the lower third position. Preheat to 350ºF (177ºC).
Thoroughly dry the surface of the beef with paper towels. Cut into 2-inch thick cubes, then season with salt and pepper, set aside. If needed, dry again before adding to the pan.
Heat a large dutch oven over medium heat. Add bacon and saute until crisp, about 6 to 7 minutes. Use a spoon to transfer the bacon to a paper towel-lined plate, reserving the fat in the pan.
Heat bacon grease over medium-high heat. Once the fat is hot, add beef to the pan in a single layer, work in two batches. Sear the beef on each side until browned, about 1 to 2 minutes per side, 6 to 8 minutes total. Transfer to the plate with the bacon. Repeat with remaining beef.
Turn heat down to medium and add the carrots, sliced onions, and pearl onions to the pan. Saute until the onions are lightly browned and tender, 10 minutes.
Add the thyme and bay leaf, saute for 30 seconds. Add the garlic, saute for 30 seconds. Add the tomato paste and saute for 30 seconds. Sprinkle in the flour, stir and cook for 1 minute. Slowly stir in the beef stock. Add in the wine, this will help the flour thicken the sauce.
Add in the browned beef and bacon, bring the liquid to a simmer for 5 minutes. Cover and carefully transfer the pot to the oven. Cook until the meat is very tender, about 1 ½ to 1 ¾ hours.
Meanwhile, prepare the mushrooms. Heat a large skillet over medium heat. Add olive oil and butter, once hot and bubbling add the mushrooms. Saute until tender and lightly browned, 5 minutes. Sprinkle with ¼ teaspoon salt, cook for 2 minutes.
When the beef is done cooking, transfer the meat and vegetables to a medium bowl. Bring the sauce to a rapid simmer over medium heat. As the fat rises to the surface, use a spoon to skim off the excess fat. Reduce the sauce until it can lightly coat the back of a spoon, about 2 to 2 ½ cups, the sauce will thicken more as it cools. Taste and season with more salt and pepper as desired.
Return the meat, vegetables, and mushrooms to the pan, stir to warm. Garnish with chopped parsley.