Paleo Apple Muffins (Made with Coconut Flour)

These paleo apple muffins are spiced with cinnamon, nutmeg, and vanilla. They’re heavy on the apples (as any good apple muffin should be, in my opinion). They taste like apple pie in muffin form and are perfect for breakfast or snack (but sweet and satisfying enough to be eaten for dessert too).

Main ingredients

These apple muffins are made with coconut flour, a nutritious grain-free flour which I love baking with. In addition to being paleo diet friendly, these apple muffins are gluten-free, grain-free, refined sugar-free, and dairy-free too.

They’re lightly sweetened with a bit of raw honey but you can substitute maple syrup if you prefer. If you have a particularly sweet tooth, you could add some raisins to the batter for some extra sweetness (about 1/2 cup is perfect).

I used pink crisp apples in these muffins because that’s what I happened to have lying around, but you can use whichever apple variety you have on hand. I will definitely be making these again with honey crisp apples as soon as they’re in season.

This recipe calls for olive oil, but you can substitute your preferred oil. Liquid coconut oil, avocado oil, or any other relatively neutral oil will work in these muffins.

These paleo apple muffins are quick and easy to whip up. They can be stored in an airtight container in the fridge for up to five days. Or feel free to double the batch and freeze some so you’ve got a stash waiting for you in the freezer when you need to grab breakfast on the run.


These muffins are so easy to make. Start by Adding the wet ingredients and spices to a large mixing bowl, then give them a good whisking. Next you’ll add the dry ingredients and mix to combine. All that’s left is to stir in the apples, divide the batter into a muffin tray, and bake. Be sure to let them cool a little before removing from the pan.

Storage and freezing

Store these muffins in an airtight container in the fridge for up to three days or freezer for up to six months.

More apple recipes

  • These sauteed apples taste like apple pie with the added bonuses of being more nutritious and easier to make.
  • Or try this gluten-free vegan apple crumble recipe. It’s perfect served with a scoop of dairy-free vanilla ice cream.
  • These vegan applesauce muffins are easy to make and delicious.
Muffins in a basket next to a wire bowl filled with apples
4.38 from 8 votes
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Paleo Apple Muffins (Made with Coconut Flour)

These paleo apple muffins are gluten-free, dairy-free, and refined sugar-free.
Course Snack
Cuisine American
Keyword clean eating, dairy-free, fall, gluten-free, paleo, refined sugar-free
Prep Time 10 minutes
Cook Time 33 minutes
Total Time 43 minutes
Servings 12
Calories 182kcal


  • 2 cups peeled and chopped raw apples
  • 1/3 cup extra virgin olive oil
  • 1/2 cup honey
  • 6 eggs
  • 1 1/2 teaspoons cinnamon
  • 1/8 teaspoon nutmeg
  • Pinch of salt
  • 1 teaspoon vanilla extract
  • 1 cup coconut flour
  • 1 teaspoon baking soda


  • Preheat the oven to 350 degrees Fahrenheit.
  • Add the eggs, honey, olive oil, cinnamon, nutmeg, salt, and vanilla extract to a large mixing bowl and use a whisk to mix well for one minute.
  • Add the coconut flour and baking soda and mix again to combine.
  • Add the apples and stir once more.
  • Spoon the batter evenly into 12 paper lined muffin cups and bake at 350 degrees Fahrenheit for 33 minutes.
  • Makes 12 paleo apple muffins.


  • You can substitute maple syrup instead of raw honey in this recipe.
  • 1/2 cup of raisins are a nice addition to the recipe if you’re craving extra sweetness.
  • Store these paleo apple muffins in an airtight container in the fridge for up to three days or freezer for up to six months.


Serving: 1Muffin | Calories: 182kcal | Carbohydrates: 21g | Protein: 4g | Fat: 10g | Saturated Fat: 3g | Cholesterol: 82mg | Sodium: 144mg | Potassium: 60mg | Fiber: 4g | Sugar: 15g | Vitamin A: 130IU | Vitamin C: 1mg | Calcium: 17mg | Iron: 1mg