Season the lean beef stew meat 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 well-browned on all sides, then remove the meat 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 is fragrant and darkened slightly.
Pour in the dry red wine to deglaze the pan, using a wooden spoon to scrape up any flavorful browned bits from the bottom.
Return the beef to the pot and pour in the beef bone broth along with the fresh thyme sprigs.
Bring the liquid to a gentle boil, then reduce the heat to low, cover, and simmer for 60 to 90 minutes until the beef is fork-tender and the sauce has thickened.