Preheat the oven to 350°F with a rack in the center position.

Season the beef all over with 2½ teaspoons of the salt and pepper.

Place the bacon in a Dutch oven or heavy-bottomed pot set over medium-low heat. Cook, stirring occasionally, until the bacon crisps and the fat is rendered, about 10 minutes. Using a slotted spoon, transfer the bacon to a paper towel–lined plate, reserving the fat in the pan.

Increase the heat to medium-high. Once the fat is just smoking, working in batches, add the beef in a single layer and cook until browned and crisp on all sides, 10 to 15 minutes. Transfer to a plate and continue with the remaining beef.

Reduce the heat to medium-low, add the yellow onion and carrot and cook, stirring occasionally, until softened, about 10 minutes. Stir in the garlic, tomato paste, bay leaf, and 1 sprig of thyme and cook until fragrant, about 1 minute more. Add in the flour and cook, stirring constantly for about 1 minute or until mostly incorporated with the fat.

Increase heat to medium-high; pour in apple vinegar and cook while scraping up any browned bits from bottom until simmering for about 5 minutes. Stir in three teaspoons of bouillon and one cup of water; bring to a simmer over high heat. Return bacon and beef along with any collected juices back into pot; cover and roast in oven until beef becomes very tender — approximately two and a half hours.

Meanwhile heat olive oil in large skillet over medium-high heat; once oil is just smoking add mushrooms and pearl onions seasoned with remaining half teaspoon of salt. Cook undisturbed until mushrooms and onions brown — around five minutes; add half cup water plus last sprig of thyme along with remaining teaspoon bouillon; bring mixture to boil then reduce heat to simmer covering it while cooking until onions become tender — roughly ten to twelve minutes.

Uncover increasing heat again high cooking while stirring frequently until vegetables caramelize which should take about two-five minutes more before serving your Beef Bourguignon garnished atop mashed potatoes if desired then sprinkling parsley.