Season the beef stew meat evenly with sea salt and black pepper.
Heat the ghee in a heavy-bottomed pot or Dutch oven over medium-high heat and sear the beef until deeply browned on all sides.
Remove the beef from the pot and set aside, then add the pearl onions, carrots, and mushrooms to the remaining fat, sautéing until the vegetables begin to soften.
Stir in the minced garlic and tomato paste, cooking for one 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.
Return the seared beef to the pot along with the beef bone broth and the sprig of fresh thyme.
Bring the liquid to a gentle simmer, then cover the pot with a tight-fitting lid and reduce the heat to low.
Cook for approximately 90 minutes or until the beef is fork-tender and the sauce has thickened into a rich glaze.