These coconut flour apple muffins are warmly spiced with cinnamon, nutmeg, and vanilla. They’re heavy on the apples (as any good apple muffin should be). They taste like apple pie in muffin form and are perfect for a nutritious breakfast or snack (but sweet and satisfying enough to be enjoyed for dessert too). These muffins are gluten free, dairy free, refined sugar free, and paleo diet friendly.
What to serve with these coconut flour apple muffins
If you’re serving these muffins at a fall-themed brunch and would like to add another option for your guests to choose from, try these paleo sweet potato muffins. They’re gluten free, dairy free, and refined sugar free.

Main ingredients and substitutions
These apple muffins are made with coconut flour, a nutritious grain-free flour which I love baking with. Definitely don’t substitute other flours in this recipe because coconut flour is much more absorbent than most other flours.
These muffins are lightly sweetened with a bit of raw honey but you can substitute maple syrup if you prefer.
I used pink crisp apples in these muffins because that’s what I happened to have on hand, but you can use any type of apple you like. I will definitely be making these again with Honeycrisp apples when they’re in season.
This recipe calls for extra virgin olive oil, but you can substitute your preferred oil. Melted coconut oil, avocado oil, or any other relatively neutral oil will work in these muffins.
How to make them
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 these muffins cool to room temperature before removing from the pan.
Optional additions
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). Chopped pecans or walnuts would be nice additions too.
Storage and freezing
These coconut flour apple muffins can be stored in an airtight container in the fridge for up to five days or in the freezer for up to six months. Then thaw at room temperature or in the microwave before serving.

More apple recipes to try
- These stovetop cinnamon apples taste like apple pie with the added bonuses of being more nutritious and easier to make.
- Or try this apple coconut flour crumble recipe. It’s perfect served with a scoop of dairy-free vanilla ice cream.
- These vegan muffins with applesauce are easy to make and delicious.
Coconut Flour Apple Muffins
Equipment
- Muffin Pan
- Paper baking cups
Ingredients
- 6 eggs
- 2 cups peeled and chopped raw apples
- 1 cup coconut flour
- 1/2 cup honey
- 1/3 cup extra virgin olive oil
- 1 1/2 teaspoons cinnamon
- 1 teaspoon vanilla extract
- 1 teaspoon baking soda
- 1/8 teaspoon nutmeg
- Pinch of salt
Instructions
- Preheat the oven to 350 degrees Fahrenheit.
- Add the eggs, honey, extra virgin olive oil, cinnamon, nutmeg, salt, and vanilla extract to a large mixing bowl, then use a whisk to mix well.
- Add the coconut flour and baking soda and use a spoon to mix.
- Add the apples and mix once more.
- Divide the batter evenly into a 12 cup muffin pan lined with paper baking cups.
- Bake at 350 degrees Fahrenheit for 33 minutes or into golden brown and a toothpick inserted into the center of a muffin comes out looking clean.
Notes
- Store these coconut flour apple muffins in an airtight container in the fridge for up to three days or freeze them for up to six months.
- You can substitute maple syrup instead of raw honey.
- Optional additions include 1/2 cup each of raisins, chopped pecans, and/or chopped walnuts.
Nutrition
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