Pat the beef chuck roast dry with paper towels and season thoroughly 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 a dark golden crust forms 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 they begin to soften and brown slightly.
Stir in the minced garlic and tomato paste, cooking for 1 minute until the paste turns a deep brick red.
Pour in the red wine to deglaze the pot, 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, fresh thyme, and bay leaf.
Bring the liquid to a gentle boil, then reduce heat to low, cover, and simmer for 60 to 90 minutes until the beef is fork-tender and the sauce has thickened into a rich glaze.