Heat the extra virgin olive oil in a heavy-bottomed pot or Dutch oven over medium-high heat.
Pat the beef chuck dry with paper towels and season with sea salt and black pepper.
Sear the beef in the pot until a deep golden-brown crust forms on all sides, then remove and set aside.
Add the chopped bacon to the pot and cook until crisp, then stir in the carrots, pearl onions, and mushrooms.
Sauté the vegetables for 5 minutes before adding the minced garlic and tomato paste, cooking for 1 minute until 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 to the pot and add the beef bone broth, thyme sprig, and bay leaf.
Bring to a gentle simmer, then cover tightly and reduce heat to low, cooking for 90 minutes until the beef is tender.
Remove the thyme sprig and bay leaf before serving the stew warm in a shallow bowl.