Pat the beef cubes dry with a paper towel and season 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 a deep golden crust forms on all sides, then remove and set aside.
In the same pot, add the halved mushrooms, sliced carrots, and pearl onions, sautéing until the vegetables are lightly browned and aromatic.
Stir in the minced garlic and tomato paste, cooking for one minute to mellow the acidity.
Pour in the dry red wine to deglaze the pot, using a wooden spoon to scrape up the flavorful browned bits from the bottom.
Return the beef to the pot and add the bone broth and fresh thyme sprig.
Bring to a gentle simmer, then reduce heat to low, cover, and cook for 90 minutes until the beef is fork-tender and the sauce has thickened into a rich glaze.