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These Paleo Apple Muffins are light and airy muffins that taste like apple cinnamon donuts! They are made using gluten-free, and dairy-free ingredients, and bake in 20 minutes!

Paleo apple muffins stacked on top of each other.

These Paleo Apple Muffins have become my new favorite homemade Fall muffin. Besides the fact that they are filled with cinnamon apple flavor, they have a great fluffy texture and almost taste like a donut. They make for a wonderful, snack, dessert, or on-the-go breakfast.

Check out my pumpkin muffins, banana oatmeal muffins, or double chocolate banana muffins for more healthy muffin ideas.

What makes these muffins great:

  • These healthy apple muffins have a delicious crumb/ streusel topping.
  • They taste amazing with a cup of tea or coffee.
  • They are made with olive oil instead of butter.
  • They taste like an apple donut ( an old fashioned one at that)!
Gluten-free apple cinnamon muffins cooling on a rack.

Recipe ingredients

  • Almond flour– blanched almond flour works best for baking. It tends to be lighter in texture and color.
  • Tapioca flour– this balances out the other flours to make it have a muffin-like texture.
  • Coconut flour– this flour is very absorbent, but paired with almond flour and tapioca flour, it results in a wonderful gluten-free bread texture.
  • Baking soda– provides a lift to baked goods.
  • Cinnamon– Ceylon cinnamon has a deeper flavor, which is great for baking.
  • Nutmeg– you can grind your nutmeg yourself or buy it ground.
  • Olive oil– extra light olive oil is best for baking.
  • Coconut sugar– this has a lower glycemic index compared to other sugars.
  • Eggs– these are binders in baked good recipes.
  • Vanilla– with or without alcohol works.
  • Apples– use your favorite Fall apple. I like using Granny Smith, Pink Lady or Honeycrisp apples.

See recipe card below for a full list of ingredients and measurements.

Additions/ Substitutions

  • Instead of tapioca flour, you can use arrowroot powder.
  • Instead of coconut sugar, you can use brown sugar. Just note, the recipe won’t be Paleo.
  • Instead of almond flour, you can use hazelnut flour.
  • Add pecans or walnuts to the batter.
  • Top the muffin with pumpkin seeds or chia seeds.
Paleo apple cinnamon muffins on a table.

Tools needed:

  • A cheese grater– you’ll need to use the largest holes of the grater.

Expert tips

  • 1) Make sure to use a combination of shredded and chopped apples. This ensures that the apple flavor is distributed but that there are also chunks of apple. ( Try my blueberry apple bread if you love chunks of apple in your baked goods)
  • 2) Using a combination of almond flour, tapioca flour and coconut flour gives these muffins great texture, while being Paleo, Gluten-free, and Grain-free.
  • 3) Use good quality spices. Cinnamon and nutmeg spices are used here. I love Ceylon cinnamon because it has a rich, deep, cinnamon smell and taste.
  • How to store: place in an airtight container or in a ziplock bag and leave at room temperature on the counter for 3 days.
  • How to freeze: individually wrap each muffin and freeze for up to 3 months.
Healthy apple muffins on a rack cooling off.

Recipe FAQs:

How are these Paleo?

A Paleo muffin is one that is grain-free, gluten-free, and dairy-free. There are no refined flours or sugars inside as well.

What kind of apple is best for these muffins?

In general, it is said that Granny Smith muffins are great for baking. I like using Pink Lady, Honeycrisp or Gala apples as well.

What can I use instead of olive oil?

Avocado oil or melted coconut oil.

A Gluten-free apple muffin cut in half on a plate.

More muffin recipes you’ll love:

Did you try this recipe? Please leave me a ⭐ review below!

5 from 9 votes

Paleo Apple Muffins

Servings: 12 muffins
Prep: 15 minutes
Cook: 20 minutes
Total: 35 minutes
Paleo apple muffins stacked on top of each other.
Light and airy muffins filled with cinnamon and apple flavors that are Grain-free and Dairy-free.


  • 1 cheese grater


Muffin ingredients:

Crumb topping ingredients:

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  • Preheat oven to 375 degrees F. Grease a 12 cup muffin pan. ( I used an olive oil spray).
  • In a medium bowl, mix the almond flour, tapioca flour, coconut flour, baking soda, salt, cinnamon and nutmeg.
  • In a large bowl, whisk or beat together the olive oil, coconut sugar, eggs, and vanilla until smooth. Stir in the chopped and shredded apples. Add half of the dry flour mixture and mix, then add the other half and mix again. Spoon the batter into the greased muffin tin.
  • Then make the crumb topping. Add 1/3 cup coconut sugar, 2 Tbs almond flour and 1/8 tsp cinnamon to a small bowl and mix. Add 1 Tbs olive oil and mix. Sprinkle the crumb topping mixture over the tops of the batter in the muffin pan.
  • Bake for 20 minutes, or until a toothpick comes out clean. Let the muffins cool in the pan for 5 minutes before letting them cool completely on a wire rack.


  • How to store: place in an airtight container or in a ziplock bag and leave at room temperature on the counter for 3 days.
  • How to freeze: individually wrap each muffin and freeze for up to 3 months.


Calories: 240kcalCarbohydrates: 20gProtein: 4gFat: 17gSaturated Fat: 2gPolyunsaturated Fat: 1gMonounsaturated Fat: 8gTrans Fat: 0.003gCholesterol: 27mgSodium: 223mgPotassium: 29mgFiber: 2gSugar: 9gVitamin A: 49IUVitamin C: 1mgCalcium: 34mgIron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Dessert
Cuisine: American
Tried this recipe?Mention @perchancetocook or tag #perchancetocook!
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  1. Made them with regular sugar, tasted amazing and the texture was so good. Hard to believe that it’s gluten free!5 stars

  2. OMG! I made these this morning thinking it would be heavy and really dense, to my amazement… these Muffins were sooo… moist and taste GREAT! After they cooled I ate one and had to freeze the rest right away so I wouldn’t eat any more. I could have easily had two more! Will be having one with coffee in the morning for sure! Thanks for sharing this recipe!5 stars

  3. fantastic. taste awesome. a healthy donut alternative. thanks for sharing and creating…you should set up a gofundme or patreon for all the work you do in testing these. I’m sure other readers would love to toss you a few dollars for the tasty healthy recipes they’ve been enjoying for years.5 stars