Step 1: Prepare and Brown the Beef

1. Season the Beef: Season the beef cubes generously with salt and black pepper.
2. Sear the Beef: In a large Dutch oven or heavy-bottomed pot, heat 1 tablespoon of olive oil over medium-high heat. Working in batches, add the beef cubes in a single layer. Sear the meat on all sides until browned, about 3-4 minutes per side. Browning the meat develops a deep flavor base for the stew. Transfer the browned beef to a plate and set aside.

Step 2: Cook the Bacon and Vegetables

1. Cook the Bacon: In the same pot, add the chopped bacon and cook until crispy, about 5 minutes. The rendered bacon fat will add a smoky flavor to the stew.
2. Sauté the Onions and Carrots: Add the diced onions and sliced carrots to the pot with the bacon. Sauté for 5-7 minutes, or until the onions are soft and lightly golden.
3. Add Garlic and Tomato Paste: Stir in the minced garlic and tomato paste. Cook for 1-2 minutes until fragrant. Tomato paste adds depth and richness to the stew.

Step 3: Create the Base of the Stew

1. Deglaze with Flour: Sprinkle the flour over the vegetable mixture, stirring well. Cook for another minute to remove the raw taste of the flour. The flour helps thicken the stew.
2. Deglaze with Red Wine: Slowly pour in the red wine, stirring and scraping up any browned bits from the bottom of the pot. This is called deglazing, and those browned bits will add flavor to the stew.
3. Add Beef Broth and Seasonings: Return the seared beef to the pot. Pour in the beef broth, add bay leaves, and sprinkle dried thyme. Bring the mixture to a gentle simmer.

Step 4: Simmer the Stew

1. Cover and Cook: Cover the pot with a lid and reduce the heat to low. Simmer the stew for 2.5 to 3 hours, or until the beef is fork-tender. Stir occasionally to ensure the ingredients are well-mixed.
2. Check for Doneness: After 2.5 hours, check the beef for tenderness. It should be melt-in-your-mouth tender, and the sauce should have thickened.

Step 5: Prepare the Mushrooms and Pearl Onions

1. Sauté Mushrooms and Pearl Onions: In a separate skillet, melt the butter over medium heat. Add the pearl onions and mushrooms, cooking until they are golden brown, about 5-7 minutes. This step enhances their flavor and keeps their texture firm.
2. Add to the Stew: Once the mushrooms and pearl onions are cooked, add them to the stew. Simmer for an additional 15-20 minutes to let the flavors meld together.

Step 6: Final Adjustments and Serve

1. Season to Taste: Taste the stew and adjust the seasoning with salt and pepper if needed.
2. Garnish and Serve: Remove the bay leaves and ladle the Beef Bourguignon into bowls. Garnish with fresh parsley, and serve over mashed potatoes, buttered noodles, or with crusty bread on the side.