Pat the beef stew meat dry with paper towels and season evenly with sea salt and black pepper.
Heat the olive oil in a heavy-bottomed pot or Dutch oven over medium-high heat.
Add the beef to the pot in a single layer and sear until deeply browned 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 fragrant and the paste turns a dark brick red.
Pour in the red wine to deglaze the pan, 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, thyme sprig, and bay leaf.
Bring the liquid to a gentle simmer, then cover the pot with a tight-fitting lid and reduce heat to low.
Cook for 75 to 90 minutes, or until the beef is fork-tender and the sauce has thickened into a rich glaze.
Remove the bay leaf and thyme sprig before serving hot in a shallow bowl.