Prepare the Beef:
Pat the beef cubes dry with paper towels and season generously with salt and pepper.
Brown the Meat:
Heat 2 tablespoons of olive oil in a Dutch oven over medium-high heat. Sear the beef in batches until browned on all sides. Remove and set aside.
Sauté Aromatics:
Add the diced onions and carrots to the pot. Cook until softened, about 5 minutes. Stir in the garlic and tomato paste, cooking for another minute until fragrant.
Deglaze with Wine:
Pour in the red wine, scraping the bottom of the pot to loosen any browned bits. Simmer for 5 minutes to reduce slightly.
Combine Ingredients:
Return the beef to the pot. Add the beef stock, bay leaf, and thyme. Bring to a gentle simmer, then cover and reduce the heat to low.
Simmer:
Cook for 1 1/2 to 2 hours, stirring occasionally, until the beef is fork-tender.
Prepare Mushrooms and Pearl Onions:
In a separate pan, heat the remaining olive oil. Sauté the mushrooms and pearl onions until golden brown. Add them to the stew during the last 30 minutes of cooking.
Thicken the Sauce (Optional):
If you prefer a thicker sauce, mix the flour with water to create a slurry. Stir it into the stew and simmer for an additional 10 minutes.
Adjust Seasoning:
Taste the stew and adjust salt and pepper as needed. Remove the bay leaf and thyme sprigs before serving.