Pat the beef chuck dry with paper towels and season evenly with sea salt and black pepper.
Heat the olive oil in a heavy-bottomed pot over medium-high heat and sear the beef until browned on all sides.
Remove the beef from the pot and add the pearl onions, sliced carrots, and halved mushrooms, sautéing until the onions are slightly translucent.
Stir in the minced garlic and tomato paste, cooking for one minute until the mixture is fragrant.
Pour in the dry red wine to deglaze the pan, using a wooden spoon to scrape up any browned bits from the bottom.
Return the beef to the pot and add the beef bone broth, fresh thyme sprig, and bay leaf.
Reduce the heat to low, cover with a tight-fitting lid, and simmer for 90 minutes or until the beef is fork-tender and the sauce has thickened into a rich glaze.