Pat the beef chuck dry with paper towels and season evenly with sea salt and black pepper.
Heat the ghee in a heavy-bottomed pot or Dutch oven over medium-high heat.
Add the beef to the pot and sear until a deep brown crust forms on all sides, then remove the beef and set aside.
Lower the heat to medium and add the mushrooms, sliced carrots, and pearl onions to the remaining fat, sautéing for 5 minutes until the vegetables begin to soften.
Stir in the tomato paste and minced garlic, cooking for 1 minute until the mixture is fragrant and slightly darkened.
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 and fresh thyme sprig.
Bring the liquid to a gentle simmer, then cover with a tight-fitting lid and reduce heat to low.
Slow-cook for 60 to 90 minutes, or until the beef is fork-tender and the sauce has reduced into a thick, glossy glaze.