Pat the beef chuck roast dry with paper towels and season evenly with sea salt and black pepper.
Heat the olive oil in a heavy-bottomed pot or Dutch oven over medium-high heat and sear the beef until deeply browned on all sides.
Remove the beef from the pot and set aside; add the pearl onions, sliced carrots, and halved mushrooms to the same pot.
Sauté the vegetables for 5 minutes until the onions begin to soften and the mushrooms release their moisture.
Stir in the minced garlic and tomato paste, cooking for 1 minute until the paste turns a dark brick red.
Pour in the red wine to deglaze the pan, using a wooden spoon to scrape up all the flavorful browned bits from the bottom.
Return the beef to the pot and add the beef bone broth, thyme sprig, and bay leaf.
Bring the liquid to a boil, then reduce heat to low, cover, and simmer for 90 minutes until the beef is tender and the sauce is glossy.