Pat the beef chuck dry with paper towels and season thoroughly with sea salt and black pepper.
In a heavy-bottomed pot or Dutch oven, cook the bacon over medium heat until crisp, then remove and set aside.
Add the olive oil to the pot and sear the beef chunks until a dark golden crust forms on all sides, then remove the beef.
Add the sliced carrot and peeled pearl onions to the pot, sautéing for 5 minutes until the onions begin to soften.
Stir in the halved mushrooms, minced garlic, and tomato paste, cooking for 2 minutes until the mixture is fragrant.
Pour in the red wine to deglaze the pot, using a wooden spoon to scrape up all the flavorful browned bits from the bottom.
Return the beef and bacon to the pot, then add the beef bone broth, fresh thyme, and the bay leaf.
Bring the liquid to a gentle simmer, then cover and reduce heat to low, cooking for 90 minutes until the beef is fork-tender and the sauce has thickened into a velvety glaze.