Pat the beef chunks 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.
Sear the beef in the hot pot until a golden-brown crust forms on all sides, then remove the meat and set it aside.
Add the sliced mushrooms, diced carrots, and pearl onions to the same pot, 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 red wine to deglaze the pan, using a wooden spoon to scrape up the flavorful browned bits from the bottom.
Return the beef to the pot and add the beef bone broth, fresh thyme, and bay leaf.
Bring the liquid to a gentle simmer, then cover the pot with a tight-fitting lid and reduce heat to low.
Braise for 60 to 90 minutes, or until the beef is fork-tender and the sauce has reduced to a thick, glossy consistency.