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 and sear the beef until a deep brown crust forms on all sides.
Remove the beef from the pot and set aside, then add the pearl onions, sliced carrots, and halved mushrooms to the remaining fat.
Sauté the vegetables for 5 minutes until the onions are translucent and the mushrooms have released their moisture.
Add the minced garlic and tomato paste to the pot, stirring constantly for 1 minute to toast the paste without burning the garlic.
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.
Stir in the beef bone broth and dried thyme, then return the seared beef and any accumulated juices back into the pot.
Bring the liquid to a gentle simmer, then cover with a tight-fitting lid and reduce heat to low, cooking for 90 minutes until the beef is fork-tender.
Garnish the finished stew with chopped fresh parsley before serving.