Heat a large Dutch oven over medium heat. Cook bacon, stirring occasionally, until fat has rendered, about 7 minutes. Remove bacon with a slotted spoon to a paper-towel lined plate and put in the fridge.

Season beef with salt and pepper. Spread out ¾ cup flour over a plate and coat the beef in flour. Turn heat to medium-high and add half the beef to the pot with the bacon fat. Cook until beef is browned, stirring to get all sides browned. Remove browned beef to a plate. Add 1 tablespoon oil if there isn’t much fat left in the pan. Brown second half of beef and remove to a plate.

Turn heat down to medium. Add remaining 1 tablespoon oil and 1 tablespoon butter. When butter is melted, add leek and carrot. Cook, stirring occasionally, until vegetables begin to soften, about 8 minutes. Add garlic and cook 2 more minutes, stirring often, until garlic is fragrant.

Add the beef back to the pot. Pour the whole bottle of wine into the pot. Use a wooden spoon to scrape up any brown bits from the bottom of the pot. Top with thyme sprigs. Turn heat to medium-high and bring to a boil. Then turn heat down to low to medium-low and cover. Let cook for about 2 hours, until beef is very tender.

When you have 15 minutes left on the beef cook time, add the frozen pearl onions and cooked bacon pieces. Stir to combine and re-cover pot. Heat a skillet over medium heat and add remaining 2 tablespoons butter. When butter is melted, add mushrooms and season with salt and pepper. Cook, stirring occasionally, until mushrooms soften, about 10 minutes. Add the mushrooms to the pot with the beef and pour any leftover butter or mushroom juices from the pan into the pot.

When beef is done cooking, remove thyme stems. Then thicken with flour. Mix remaining 2 tablespoons flour with ¼ cup cold water. Mix very thoroughly so flour is completely dissolved with no lumps. Pour into the pot with the beef and stir. Turn heat up and simmer 5 more minutes, to cook out the starchy flour taste.

Serve stew with something to soak up the sauce, like boiled potatoes, egg noodles, or bread. Garnish with chopped parsley.