Heat the oven: Preheat the oven to 325°F (165°C). Pat the beef very dry with paper towels. Season it with 1/2 teaspoon of the kosher salt and 1/4 teaspoon of the black pepper.

Render the bacon: Heat a 6- to 7-quart Dutch oven over medium heat. Add the bacon and cook for 5–7 minutes, stirring occasionally, until browned and the fat has rendered. Transfer the bacon to a plate, leaving about 2 tablespoons of fat in the pot.

Brown the beef: Increase the heat to medium-high: Working in batches, add the beef without crowding the pot. Brown for about 2–3 minutes per side, turning until several surfaces are deeply browned. Transfer the beef to the plate with the bacon. Add a small amount of olive oil if the pot becomes dry.

Cook the vegetables: Reduce the heat to medium: Add the chopped onion and carrots and cook for 5–6 minutes, stirring occasionally, until the onion softens and begins to brown. Add the garlic and tomato paste and cook for 1 minute. The tomato paste should darken slightly and coat the vegetables.

Deglaze with wine: Pour in 1 1/2 cups (360 mL) of the red wine. Scrape the bottom of the Dutch oven with a wooden spoon to loosen the browned bits. Simmer for 3–4 minutes, until the wine reduces slightly and the strong raw alcohol aroma has softened.

Build the braise: Return the browned beef and bacon to the pot. Add the beef broth, bay leaves, and thyme. The liquid should come roughly halfway to two-thirds up the beef rather than completely covering it. Bring the liquid to a gentle simmer.

Braise the beef: Cover the Dutch oven and transfer it to the oven. Cook for 2 hours, or until the beef is becoming very tender but still holds its shape. Check after about 1 1/2 hours; the liquid should be gently bubbling, not boiling aggressively.

Prepare the mushrooms and onions: While the beef braises, heat the olive oil in a large skillet over medium-high heat. Add the pearl onions and mushrooms and cook for 7–9 minutes, stirring occasionally, until browned and lightly tender. Remove from the heat.

Thicken the sauce: Remove the Dutch oven from the oven. Carefully transfer the beef and vegetables to a large bowl with tongs. Discard the bay leaves and thyme stems. Whisk the flour into the remaining 1/2 cup (120 mL) red wine until smooth, then stir it into the braising liquid.

Finish the braise: Return the beef mixture to the Dutch oven along with the browned pearl onions and mushrooms. Cover and return to the oven for another 30–40 minutes, until the beef is fork-tender and the sauce has thickened enough to coat the back of a spoon.

Check seasoning and consistency: Remove the pot from the oven and discard any remaining herb stems. Taste the sauce and add the remaining 1/2 teaspoon kosher salt and 1/4 teaspoon black pepper as needed. If the sauce is thinner than desired, simmer the uncovered stew on the stovetop over medium-low heat for 5–10 minutes.

Rest and serve: Let the Beef Bourguignon rest uncovered for about 20 minutes before serving. Sprinkle with chopped parsley if using. Serve warm with mashed potatoes, crusty bread, or buttered noodles.