Preheat your oven to 350°F. In a large heavy-bottomed Dutch oven or braising pot, cook the bacon pieces over medium-high heat until crispy, about 5-7 minutes. Remove the bacon with a slotted spoon and set aside, leaving the rendered fat in the pot. Pat the beef cubes dry with paper towels and season generously on all sides with kosher salt and freshly cracked black pepper. Working in batches to avoid crowding, sear the beef in the bacon fat until deeply browned on all sides, about 3-4 minutes per batch. Remove each batch to a plate as it finishes—don’t worry about cooking it through, we’re just building color and flavor here. This browning creates the foundation for a rich, complex sauce.

Add the 2 tablespoons of butter to the pot and let it foam slightly. Add the diced onion and chopped carrots, cooking for 2-3 minutes, stirring occasionally, until they soften slightly and begin to pick up some color. Add the minced garlic and cook for another minute until fragrant. Stir in the tomato paste and cook for 2-3 minutes, allowing it to caramelize slightly in the pot—this deepens its flavor significantly. Sprinkle the flour over everything and stir constantly for another 2-3 minutes to cook out the raw flour taste and create a roux base that will thicken our sauce.

Pour the burgundy wine into the pot, scraping the bottom with a wooden spoon to release all the caramelized bits stuck to the pan—this fond is liquid gold and contains concentrated flavor. Stir in the beef broth and beef bouillon base, which will add depth and umami to the braise. Return the seared beef and the reserved bacon to the pot, and add the thyme sprigs and bay leaves. Bring everything to a gentle simmer over medium heat, then cover the pot with a tight-fitting lid and transfer it to the preheated 350°F oven. I prefer using fresh bay leaves here because they impart a more delicate, complex flavor compared to dried ones.

Allow the beef to braise in the oven for 2.5 hours, covered. While it braises, prepare the mushrooms and pearl onions so they’re ready to add halfway through. Melt 2 tablespoons of butter in a large skillet over medium-high heat. Once foaming, add the cremini mushroom pieces and cook without stirring for 3-4 minutes to develop a golden-brown crust, then stir and continue cooking until all sides are browned, about 5-7 minutes total. Add the thawed pearl onions to the skillet and cook together for another 5 minutes, then season with a pinch of salt and pepper. Set this mixture aside until needed.

Remove the pot from the oven after 2.5 hours and carefully stir in the mushrooms and pearl onions from Step 4, distributing them evenly throughout the braise. Cover the pot again and return it to the oven for another 45-60 minutes, until the beef is fork-tender and the flavors have melded beautifully. The extended cooking time allows the mushrooms and pearl onions to absorb the rich braising liquid while the beef becomes melt-in-your-mouth tender.

Remove the pot from the oven and let it rest, covered, for 30 minutes at room temperature. This resting period allows the beef to relax and reabsorb its juices, ensuring maximum tenderness and flavor. During this time, the sauce will also settle and any excess fat will rise to the surface where you can skim it off if desired. Taste the braising liquid and adjust seasoning with additional salt and pepper as needed. Serve the beef bourguignon directly from the pot or in a serving dish, making sure each portion gets plenty of beef, vegetables, mushrooms, and rich sauce.