Pat the beef chuck roast dry with paper towels and season all sides evenly with the sea salt and black pepper.
In a heavy-bottomed pot or Dutch oven, melt the ghee over medium-high heat and sear the beef until deeply browned on all sides, then remove to a plate.
Add the chopped bacon to the same pot and cook until crisp, then stir in the halved cremini mushrooms, sliced carrots, and pearl onions.
Sauté the vegetables for 5 to 7 minutes until the mushrooms are golden and the onions soften, then stir in the minced garlic and tomato paste for 1 minute.
Pour in the dry red wine to deglaze the pan, using a wooden spoon to scrape up all the flavorful browned bits from the bottom of the pot.
Return the beef and any accumulated juices to the pot, pour in the bone broth, and tuck in the fresh thyme sprig.
Cover with a tight-fitting lid and simmer on low heat for 90 minutes, or until the beef is fork-tender and the sauce has reduced into a velvety glaze.