Pat the beef chuck dry with paper towels and season with sea salt and black pepper.
In a heavy-bottomed pot or Dutch oven, cook the nitrate-free bacon over medium heat until crisp, then remove and set aside.
Add the extra virgin olive oil to the pot and sear the beef cubes until deeply browned on all sides, then remove and set aside.
Add the pearl onions, carrots, and cremini mushrooms to the pot, sautéing until the vegetables are slightly softened and browned.
Stir in the minced garlic and tomato paste, cooking for 1 minute until fragrant.
Pour in the dry red wine to deglaze the pot, scraping up any browned bits from the bottom with a wooden spoon.
Return the beef and bacon to the pot, then add the beef bone broth and the sprig of fresh thyme.
Cover the pot and simmer on low heat for 90 minutes, or until the beef is fork-tender and the sauce has thickened.