Pat the beef chuck 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.
Sear the beef chunks until deeply browned on all sides, then remove and set aside on a plate.
In the same pot, add the pearl onions, sliced carrots, and halved cremini mushrooms, sautéing for 5 minutes until the vegetables begin to soften.
Stir in the minced garlic and tomato paste, cooking for 1 minute until the mixture is fragrant and slightly darkened.
Pour in the dry red wine to deglaze the pot, using a wooden spoon to scrape up any browned bits from the bottom.
Return the beef and any accumulated juices to the pot, then pour in the beef bone broth.
Add the fresh thyme sprig and bay leaf, then bring the liquid to a gentle simmer.
Cover the pot tightly and reduce heat to low, simmering for 90 minutes until the beef is fork-tender.
Remove the bay leaf and thyme sprig before serving hot in a shallow bowl.