Pat the beef top round 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.
Sear the beef cubes in the hot ghee until a deep brown crust forms on all sides, then remove the beef and set aside.
In the same pot, add the pearl onions, sliced carrots, and halved cremini mushrooms, 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 the paste darkens slightly.
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.
Return the seared beef to the pot and pour in the beef bone broth until the ingredients are mostly submerged.
Add the fresh thyme sprig and bay leaf, then bring the liquid to a gentle simmer.
Cover the pot and reduce the heat to low, simmering for 90 minutes or until the beef is fork-tender and the sauce has reduced into a thick glaze.