In a heavy-bottomed pot or Dutch oven, cook the chopped bacon over medium heat until the fat renders and the bacon is crisp.
Remove the bacon with a slotted spoon and set aside, leaving the fat in the pot, then add the ghee.
Pat the beef cubes dry, season with sea salt and black pepper, and sear in the pot until a deep brown crust forms on all sides.
Remove the beef and add the pearl onions, sliced carrots, and halved mushrooms to the pot, sautéing for 5 minutes until slightly softened.
Stir in the minced garlic and tomato paste, cooking for 1 minute until fragrant and the paste darkens.
Pour in the red wine to deglaze the pot, scraping up the browned bits, then add the beef bone broth, seared beef, bacon, and the thyme sprig.
Bring to a gentle simmer, then reduce heat to low, cover, and cook for 90 minutes until the beef is tender and the sauce has reached a glossy consistency.