Pat the beef stew meat 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.
Add the beef to the pot and sear until a deep brown crust forms on all sides, then remove the beef and set aside.
In the same pot, add the pearl onions, sliced carrots, and halved 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 becomes fragrant and darkens slightly.
Pour in the dry red wine to deglaze the pot, using a wooden spoon to scrape up all the flavorful browned bits from the bottom.
Add the beef bone broth, fresh thyme, and the bay leaf, then return the seared beef and any accumulated juices to the pot.
Bring the liquid to a gentle simmer, then reduce heat to low, cover, and cook for 90 minutes until the beef is fork-tender.
Discard the bay leaf and serve the stew warm in a shallow bowl.