Gather the ingredients. Position a rack in the lower third of the oven and heat to 325 F.

Put 8 ounces thick-cut bacon or pancetta, coarsely chopped in a large Dutch oven or other heavy-duty oven proof pot and cook over medium-high heat, stirring occasionally, until brown and crisp, about 8 minutes. Transfer the bacon to a large rimmed plate with a slotted spoon, leaving the fat in the pot. Slide the pot off the heat.

Pat 3 pounds chuck roast, cut into large (2-inch) chunks dry with paper towels. Season the meat with 1 teaspoon fine salt and ½ teaspoon freshly ground black pepper and toss with ⅓ cup all-purpose flour to coat evenly.

Return the pot to medium-high heat. Add a handful of the beef to the pot, brushing off the excess flour as you work. Don’t overcrowd the meat, making sure there is space in between each chunk, or it will sweat in its own juices instead of browning. Let the meat cook for 3 minutes without moving it, flip with tongs, and continue to brown until you have a deep golden brown crust on the second side, about 2 minutes. Transfer the browned meat to the plate with the bacon. Decrease the heat if the brown bits on the bottom of the pot begin to burn.

Repeat the browning process with the rest of the meat in 2 to 3 more batches, placing the pieces on the plate with the already browned meat as you work. Discard any excess flour.

Add 1 medium yellow onion, coarsely chopped and 1 large carrot, cut crosswise into 1 ½-inch long pieces to the pot; saute until the vegetables begin to brown, about 4 minutes. Add 4 medium garlic cloves, peeled and left whole and cook, stirring constantly, until fragrant, about 1 minute.

Carefully add ½ cup Cognac or brandy , raise the heat to high, and boil, scraping the brown bits from the bottom of the pot, until nearly evaporated, about 1 minute.

Add 2 tablespoons tomato paste and stir to combine. Stir in 2 cups low-sodium beef broth and 2 cups dry red wine and bring to a boil over high heat. Add the browned beef, bacon, any accumulated juices on the plate, 2 teaspoons chopped fresh thyme or ½ teaspoon dried thyme , and 2 bay leaves and stir to combine.

Cover with a tight-fitting lid and slide the pot into the oven. Bake until the beef is very tender, about 2 hours. You should be able to cleave a chunk of beef in half easily with a fork.

During the last 30 minutes of baking time, make the onion and mushroom garnish. Bring a small saucepan of water to a boil. Trim the tips (opposite the root end) off 8 ounces (about 1 ½ cups) pearl onions .

Add the onions to the boiling water and cook for 2 minutes. Drain.

When cool enough to handle, squeeze the onions at the root end. The onions will pop out of their skins. Discard the skins.

Melt 2 tablespoons unsalted butter in a large skillet over medium heat. Add the onions and 8 ounces cremini mushrooms, quartered and saute until they begin to brown, about 8 minutes.

Add the remaining ½ cup low-sodium beef broth and 1 teaspoon granulated sugar . Cover and simmer over medium-low heat until the onions are tender when pierced with a fork, 10 to 15 minutes. Uncover and continue to simmer until the liquid is mostly evaporated and it becomes a syrupy glaze, 3 to 5 minutes more. Remove from the heat.

When the beef is done, remove the pot from the oven, uncover, and let it stand for 10 minutes.

Skim any clear fat that has risen to the top of the sauce, if desired. Stir the pearl onions and mushrooms into the pot. Taste and adjust the seasoning with salt and pepper, if needed. Serve garnished with 2 tablespoons finely chopped fresh parsley .