Preheat the oven to 325°F (165°C).
In a large Dutch oven or oven-safe pot, cook the chopped bacon over medium heat until crispy. Remove the bacon and set it aside, leaving the bacon fat in the pot.
Pat the beef dry with paper towels and season it with salt and pepper. Brown the whole beef chuck roast in the bacon fat on all sides until nicely seared or about 3-4 minutes per side. Remove the beef and set it aside.
Add olive oil to the pot if needed, then sauté the onion, garlic, potatoes and carrots until they begin to soften, about 5-10 minutes.
Pour in the red wine, scraping up any browned bits from the bottom of the pot. Add the beef broth, tomato paste, thyme, oregano, bay leaves, and the cooked bacon. Bring the mixture to a simmer.
Return the seared whole beef chuck roast to the pot. Cover and place it in the preheated oven for about 4 hours, or until the beef is tender.
Optional: In a separate pan, melt butter over medium heat. Add the quartered mushrooms and sauté until they release their juices and start to brown.
Once the beef is tender, remove the pot from the oven. Take out the beef and vegetables, leaving the liquid in the pot.
Mix flour and water to form a paste. Whisk this paste into the liquid in the pot to thicken the sauce. Simmer for a few minutes until the sauce thickens.
Return the whole beef chuck roast and vegetables to the pot. Add the sautéed mushrooms. Stir gently to combine and heat through for a few minutes.
Season with additional salt and pepper if needed. Remove the bay leaves.
Serve the beef bourguignon hot, garnished with chopped parsley. It pairs wonderfully with mashed potatoes, crusty bread, or mashed cauliflower.