Arrange a rack in the lower third of the oven and heat the oven to 350℉.

Dice 1 large yellow onion (about 2 cups). Peel and cut 1 medium carrot crosswise into ½-inch-thick rounds (about ⅓ cup). Mince 3 garlic cloves.

Cut 8 ounces thick-cut bacon crosswise into ½-inch pieces. Place in a Dutch oven or other large heavy-bottomed oven-safe pot with a tight-fitting lid. Cook over medium heat, stirring occasionally, until the fat is rendered and the bacon is browned and crisp, 10 to 12 minutes. Meanwhile, trim any excess fat from 1 (3-pound) boneless beef chuck roast, then cut into rough 2-inch cubes. Pat dry with paper towels and season all over with 2 teaspoons of the kosher salt and ½ teaspoon of the black pepper.

When the bacon is ready, use a slotted spoon to transfer to a large bowl or plate.

Add half of the beef to the pot in a single layer and cook until browned on all sides, 2 to 3 minutes per side. Use tongs to transfer to the bowl or plate with the bacon. Repeat with browning the remaining beef and transferring to the plate. The beef will not be cooked through.

Add the onion and carrot to the pot and cook, stirring occasionally, until the onion is softened, about 3 minutes. Add the garlic and cook until fragrant, about 30 seconds. Add 1 tablespoon tomato paste and stir to coat the vegetables. Cook until darkened in color, 1 to 2 minutes. Sprinkle with 3 tablespoons all-purpose flour. Stir to coat and cook for 1 minute to cook the floury taste out.

Add 1 (750-ml) bottle dry red wine and scrape up any browned bits from the bottom of the pot with a wooden spoon. Add 1 cup low-sodium beef broth, 5 fresh thyme sprigs, 2 dried bay leaves, and ½ teaspoon of the kosher salt. Return the beef, bacon, and any accumulated juices to the pot and stir to combine. Increase the heat to medium high and bring to a simmer.

Cover the pot and transfer to the oven. Cook until the beef is very tender, about 2 hours. About 30 minutes before the beef is ready, trim and peel 8 ounces pearl onions if needed, and quarter 8 ounces cremini mushrooms.

Melt 3 tablespoons unsalted butter in a large skillet over medium heat. Add the onions, mushrooms, remaining ½ teaspoon kosher salt, and remaining ¼ teaspoon black pepper. Cook, stirring occasionally, until tender and lightly browned all over, 12 to 15 minutes.

Add the cooked onions and mushrooms to the pot and stir to combine. Remove and discard the bay leaves and thyme stems. Taste and season with more kosher salt and black pepper as needed. Garnish with chopped fresh parsley leaves if desired.