Heat 2 tablespoons oil in a large skillet over medium-high heat. Add the beef cubes and brown on all sides, then transfer them to the slow cooker.
Add the onions, carrots, potatoes, and garlic to the slow cooker. Sprinkle the 2 tablespoons flour, thyme, 1 teaspoon salt, and pepper over the meat and vegetables.
Pour in the Guinness and beef broth. Stir gently to combine everything.
Cover and cook on low for 8 hours until the beef is fork-tender.
About 30 minutes before the stew is done, heat the oven to 425°F. Divide the 2 tablespoons oil among 4 cups of a muffin tin and place the tin in the oven to heat.
In a mixing bowl, whisk together 1 cup flour, 2 eggs, milk, and 1/2 teaspoon salt until smooth. Let the batter rest 10 minutes.
Carefully remove the hot muffin tin from the oven. Pour the batter evenly into the 4 oiled cups. Bake for 20 minutes until the puddings are puffed and golden.
Ladle the stew into bowls and place one Yorkshire pudding on top of each serving.