Pat the beef chuck dry with paper towels and season evenly with sea salt and black pepper.
In a heavy-bottomed pot or Dutch oven, heat the olive oil over medium heat and cook the chopped bacon until crisp.
Remove the bacon with a slotted spoon, leaving the rendered fat in the pot, and increase heat to medium-high.
Sear the beef cubes in batches until a deep brown crust forms on all sides, then remove and set aside.
Add the pearl onions, sliced carrots, and halved mushrooms to the pot, sautéing for 5 minutes until the vegetables begin to soften.
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 all the 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 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 the stew warm in a shallow bowl.