Pat beef chuck cubes very dry with paper towels. Season generously with salt and pepper. Toss the beef with flour until lightly coated.

Preheat your oven to 325°F (160°C). In a large Dutch oven over medium-high heat, cook the diced bacon until crisp. Remove bacon with a slotted spoon and set aside, leaving the rendered fat in the pot.

Add 1 tablespoon of olive oil to the Dutch oven with the bacon fat if needed. Brown the floured beef cubes in batches, about 2-3 minutes per side, until deeply colored. Do not overcrowd the pot. Remove seared beef and set aside with the bacon.

Reduce heat to medium. Add the remaining 1 tablespoon of olive oil (if needed), chopped yellow onion, carrots, and celery to the pot. Sauté for 5-7 minutes until softened, scraping up any browned bits from the bottom of the pot. Add minced garlic and tomato paste, cooking for another 1-2 minutes until fragrant.

Pour in the red wine, scraping the bottom of the pot with a wooden spoon to deglaze and release all the flavorful brown bits. Bring to a simmer and cook for 5-10 minutes, allowing the alcohol to cook off and the wine to reduce slightly.

Return the seared beef and cooked bacon to the Dutch oven. Stir in the beef broth, bay leaf, and dried thyme. Bring the mixture to a gentle simmer on the stovetop.

Cover the Dutch oven tightly with a lid. Transfer to the preheated oven and braise for 2 to 2.5 hours, or until the beef is very tender and easily pierced with a fork.

After the beef has braised for 2 to 2.5 hours, add the cremini mushrooms and pearl onions to the pot. Stir gently, cover, and return to the oven for another 30 minutes, or until the vegetables are tender.

Remove the bay leaf. Taste and adjust seasoning if necessary. Ladle the One Pot Beef Bourguignon into bowls. Garnish with fresh chopped parsley and serve hot, perhaps with crusty bread, mashed potatoes, or egg noodles.