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 large heavy-bottomed pot or Dutch oven over medium-high heat.
Add the beef in a single layer and sear 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 mushrooms, sautéing for 5 minutes until the vegetables begin to soften.
Stir in the minced garlic and tomato paste, cooking for 1 minute until fragrant and the paste turns a dark brick red.
Pour in the dry red wine to deglaze the pot, scraping up all the flavorful browned bits from the bottom with a wooden spoon.
Return the beef and any accumulated juices to the pot, then pour in the beef bone broth until the meat is mostly submerged.
Add the fresh thyme sprig and dried bay leaf, bring to a gentle simmer, then cover and cook on low heat for 90 minutes until the beef is fork-tender.
Remove the thyme sprig and bay leaf before serving the stew warm in shallow bowls.