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Preheat the oven to 325 F. Line a muffin tray with liners and set aside.
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In a large bowl, beat the butter, maple syrup and egg together until well combined. Stir in the vanilla extract.
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In a separate bowl, combine the flour, baking powder, baking soda, salt, cinnamon, nutmeg, pumpkin seeds, sunflower seeds and chia seeds. Mix together.
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Peel your apples. Grate two of the apples and finely chop the other apples.
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Combine the butter mixture, the flour mixture and the prepared apples all-together in the large bowl. Stir until everything is well combined and all the flour is absorbed.
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Fill your muffin liners about 2/3 full and bake for 20 minutes until cooked through. Use a toothpick to check for doneness. Allow the cupcakes to cool for 10 minutes in the tray before transferring to a cooling rack.
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Store in an air tight container for up to 5 days or freeze and take them out as needed.