Pat the beef chuck roast dry with paper towels and season evenly with sea salt and black pepper.
Heat the extra virgin olive oil in a heavy-bottomed pot or Dutch oven over medium-high heat and sear the beef until a dark golden crust forms on all sides.
Remove the beef from the pot and set aside, then add the pearl onions, sliced carrot, and celery to the remaining fat, sautéing until the onions are translucent.
Stir in the halved mushrooms and minced garlic, cooking for 3-5 minutes until the mushrooms begin to brown and release their moisture.
Add the tomato paste and cook for 1 minute before pouring in the red wine, using a wooden spoon to scrape up all the flavorful browned bits from the bottom.
Pour in the beef bone broth and return the seared beef to the pot along with the fresh thyme sprig and bay leaf.
Bring the liquid to a gentle simmer, then cover with a tight-fitting lid and reduce heat to low, cooking for 90 minutes until the beef is fork-tender.
Discard the bay leaf and thyme sprig before serving the braised beef and vegetables in a shallow bowl.