Pat the beef dry with paper towels. Season the beef stew meat generously with salt and black pepper.
Heat 1.5 tablespoons of olive oil in a large Dutch oven or heavy-bottomed pot over medium-high heat. Add the beef in batches, searing on all sides until browned. Remove and set aside.
Add the remaining olive oil to the pot and sauté the chopped onion until softened, about 3–4 minutes.
Stir in the apple cider vinegar, scraping the bottom of the pan to loosen any browned bits. Sprinkle the flour over the onions and stir well to coat, cooking for 1 minute.
Gradually pour in the apple cider juice and beef broth, stirring constantly to combine and prevent lumps. Add the dried thyme, bay leaves, and the seared beef back to the pot.
Bring the mixture to a boil, then reduce the heat to low. Cover and let simmer for 1 hour, stirring occasionally.
Stir in the potatoes, carrots, and celery. Continue to simmer for another 30–40 minutes, or until the vegetables are tender and the beef is fully cooked.
Remove the bay leaves before serving. Garnish with fresh thyme sprigs, and serve warm in a bowl with crusty bread or, if desired, over rice.