Preheat the oven to 350 degrees Fahrenheit (175 degrees Celsius).
Gather the ingredients.
Wash the apples well.
Using an apple corer, core the center of each apple, going ¾ down the apple. The bottom of the apple should remain closed.
Using a curved paring knife, cut a round shape in each apple creating a small bowl. That is where the filling will go. Make sure to remove all pits.
Place the carved apples in water to prevent them from turning black.
Cut the pieces of apple, that you removed from each center, into small cubes removing the remaining pits & peels.
Place the pieces into a small bowl.
Add the almond butter, honey & cinnamon and mix well.
Add the pomegranate seeds and almond flakes and mix well.
Fill the center of the apples with the mixture and place them in the baking pan.
Pour any remaining liquid from the mixture into the apples.
Add ½ a cup of water to the bottom of the pan.
Cover with a baking sheet and bake for 45 minutes.
Uncover the apples, continue to bake for 15 minutes or until the apples are tender.
Keep refrigerated.