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 bacon over medium heat until crispy, then remove and set aside, leaving the rendered fat in the pot.
Add the olive oil to the pot and sear the beef chunks on all sides until a golden-brown crust forms, then remove the beef and set aside.
Add the pearl onions, sliced carrots, and halved mushrooms to the pot, sautéing for 5-7 minutes until the vegetables begin to soften and brown.
Stir in the minced garlic and tomato paste, cooking for 1 minute until fragrant.
Pour in the red wine to deglaze the pan, 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, thyme sprig, and bay leaf.
Bring the liquid to a gentle simmer, then cover and reduce heat to low, cooking for 90 minutes or until the beef is fork-tender.
Remove the bay leaf and thyme sprig before serving hot in a shallow bowl.