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Coconut Flour Apple Cinnamon Muffins Recipe (Grain Free)

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gluten free apple cinnamon muffins recipe
Wellness Mama » Blog » Recipes » Breakfast Recipes » Coconut Flour Apple Cinnamon Muffins Recipe (Grain Free)

I discovered this grain-free apple cinnamon muffin recipe out of desperation, really. (Isn’t it so true that necessity is the mother of invention?)

On this particular morning I realized I only had five eggs in the fridge — not even close to enough to feed us all, especially when each kid could easily eat three each! I had coconut flour, homemade applesauce, and coconut oil on hand, so I mixed them and … voilà!

The kids requested them every day at breakfast for a week straight, and a great go-to (and also “to-go”) breakfast recipe was born!

Paleo Apple Cinnamon Muffins: A Break from the Norm

I’ll be real here… I haven’t always been a great baker, which I guess makes sense considering we don’t often eat grains. Still, being grain-free can mean a lot of scrambled eggs for breakfast, and we all have those days when only baked goods will do.

It always feels great to get it right and hit on a recipe that makes both mom and kids happy.

If you haven’t had coconut flour muffins before, know that they turn out a little smaller and denser than your typical muffin. Still, they have that bready texture and aroma. They’re full of protein and fiber that really satisfy, not to mention all the great health benefits of coconut since these muffins use both coconut flour and coconut oil.

These apple cinnamon muffins stay in regular rotation at our house and even kick off the breakfast section in my Wellness Mama Cookbook. As with almost all of the recipes in my cookbook, this muffin recipe takes 30 minutes or less to make, uses real food ingredients, and doesn’t generate a lot of dirty dishes to wash up afterward.

If you have to be careful and rotate recipes for allergy reasons or are just looking to get more variety at breakfast, check out the Real Plans meal planning tool for more help.

Apple Cinnamon … or Whatever Flavor You Desire!

I chose this applesauce and cinnamon combo out of convenience, but these muffins are incredibly versatile. I even discovered with a few simple modifications I could turn this recipe into these coconut flour apple cinnamon pancakes!

Using either the muffin or pancake recipe as a base, try these mix-ins to change things up from time to time:

  • Reduce the applesauce by ¼ cup and add an overripe banana before blending
  • Stir in ½ cup toasted chopped nuts, such as walnuts, by hand
  • Mix in ½ cup fresh or frozen blueberries or raspberries
  • Add ½ cup chopped apples for a little extra texture
  • Add 3 tablespoons cocoa powder to make almost cupcake-like muffins
  • Top with shredded coconut before baking for extra crunch
  • Skip the apple and make them orange cranberry or lemon blueberry muffins!

The Recipe

gluten free apple cinnamon muffins recipe

Coconut Flour Apple Cinnamon Muffins

Hearty breakfast muffins that can be personalized to your specific tastes.
Prep Time 5 minutes
Cook Time 15 minutes
Total Time 20 minutes
Calories 129kcal
Author Katie Wells





  • Preheat the oven to 400°F.
  • Grease a muffin pan with coconut oil or use silicone muffin cups like these.
  • Mix all ingredients in a medium-sized bowl with an immersion blender or whisk until well mixed. I prefer the immersion blender so the coconut oil mixes evenly even if cold/hard.
  • Let sit 5 minutes. This helps the coconut flour absorb moisture and creates a better texture in the finished muffins.
  • Use 1/3 cup measure to scoop into muffin tins.
  • Bake 12-15 minutes until starting to brown and not soft when lightly touched on the top.
  • Let cool 2 minutes, drizzle with honey (if desired) and serve.


Nutrition Facts
Coconut Flour Apple Cinnamon Muffins
Amount Per Serving (1 muffin)
Calories 129 Calories from Fat 67
% Daily Value*
Fat 7.4g11%
Saturated Fat 5.2g33%
Cholesterol 68mg23%
Sodium 130mg6%
Carbohydrates 12.9g4%
Fiber 4.9g20%
Sugar 5.1g6%
Protein 3.7g7%
* Percent Daily Values are based on a 2000 calorie diet.


If you frequently need breakfast to-go, try making a large batch of these and freezing them.

Like this recipe? Check out my new cookbook, or get all my recipes (over 500!) in a personalized weekly meal planner here!

Easy Coconut Flour Apple Cinnamon Muffins

Missing baked goods? Try these other favorite grain-free breakfast recipes:

Have you ever tried making grain-free muffins? What other variations can you think of? Please share below!

Katie Wells Avatar

About Katie Wells

Katie Wells, CTNC, MCHC, Founder of Wellness Mama and Co-founder of Wellnesse, has a background in research, journalism, and nutrition. As a mom of six, she turned to research and took health into her own hands to find answers to her health problems. WellnessMama.com is the culmination of her thousands of hours of research and all posts are medically reviewed and verified by the Wellness Mama research team. Katie is also the author of the bestselling books The Wellness Mama Cookbook and The Wellness Mama 5-Step Lifestyle Detox.


333 responses to “Coconut Flour Apple Cinnamon Muffins Recipe (Grain Free)”

  1. Carol Avatar

    Thank you for these!!! Healthier food choices? Yes, please! Mine just came out from the oven and they look fabulous and delish.

  2. Rachel Avatar

    We have a person in the family who has autism…they really love the Cinamon Apple muffins!

  3. Sherri Dunlap Avatar
    Sherri Dunlap

    Hi, I’m interested in trying these but do you happen to have the nutrition breakout?
    i.e., how many calories, protein, carbohydrates, sugar, etc?

    Thank you,

  4. Pam Avatar

    Do these have to be refrigerated? I am going on vacation and these sound like a great snack to take along.

  5. Doris Avatar

    Thanks so much for this recipe! I recently bought a bag of coconut flour and have been trying to find some good recipes for it.

  6. Ashley Avatar

    Hi I bought unrefined Virgin coconut oil but it only bakes up to 280 degrees. Should I just bake it at 400 still?

  7. emily Avatar

    5 stars
    Made this as a cake, put a ribbon of apple butter through it with a knife after I put it in the cake pan, it came out awesome! Love it, a nice moist cake, not too sweet, very satisfying! It’s a keeper in my home.

  8. verena Avatar

    That looks really good, I do a very similar one and I add one banana to the mix

  9. Bert Avatar

    Just made these for breakfast. Followed the recipe except used my food processor to grate 2 fresh Braeburn apples. Then switched to the dough blade and added all the other ingredients. Just for interest I added a handful of raw unsweetened coconut flakes and sprouted almonds. Baked them for 18 mins. They were fantastic. Thanks!

  10. Carol Avatar

    These sound SO wonderful! I just ordered some coconut flour from Tropical Traditions, and can’t wait to use it! I was trying to find a good recipe to make something for the grandkids for Easter, and these sound just perfect.
    Read all the comments and got some other good ideas as well, so thanks to all of you, and especially you, WellnessMama for your wonderful recipes and great posts!!!

  11. Grace Avatar

    These were so light and airy. Loved them. Not too sweet either so I went ahead with your suggestion to drizzle a bit of honey on top 🙂

  12. Michelle Avatar

    Thank you for your detailed recipe for someone who isn’t having much success making healthy gluten free recipes! I would not know to let a mix sit for five minutes before cooking. I’m learning so much from you!

  13. AnnaA Avatar

    4 stars
    Just tried making these as instructed, except using the banana and walnut combo and replacing the eggs with chia seeds soaked in water as we don’t eat eggs. They have so far been in the oven for 25 mins and even though a skewer is coming out clean, they don’t look cooked judging by the top and sides. What am I doing wrong? 🙁

    1. Caldwella Avatar

      It doesn’t look cooked, but there is nothing dangerously “raw” to worry about. It is probably an issue of too much “wet” and not enough dry and leavening agents. I think when a recipe calls for 5 eggs, it is hinging on the use of those eggs to make it work. That is the major ingredient. I think instead of trying to sub ingredients in a certain recipe, try finding one that already starts with using the chia seeds as the “egg”. I think the results are better. Otherwise, you just risk having to experiment a lot and probably end up changing the whole recipe in the process.

  14. Julie Harper Avatar
    Julie Harper

    Did not work for me:( followed the recipe and i used unsweetened Mott’s apple sauce…. The muffins were soft (i left them in the oven an extra 5 minutes) and broke apart too easily and the bottoms were very oily:(

    1. Susan Avatar

      I tried this too.. however, I did forget the baking soda…I did everything to the letter (used store bought organic apple sauce). and not only did it stick, they tasted horrible.. I had to leave them in for 30 mins extra.. they were not cooking… tasted like cinnamon dirt.. lol.. what did I do wrong???? you said you don’t actually need the baking soda or powder. what happened???

  15. GiGi Avatar

    5 stars
    I have been experimenting with coconut flour a lot lately and I am obsessed with it! I think I am going to try making lemon poppyseed muffins next 🙂 Stevia, Lemon, Coconut Flour, Poppy Seeds – Maybe some coconut oil and flax to make them all stick together – YUM 🙂

  16. JGB Avatar

    Just made these for my kids this am and they are delicious! Thanks for such an awesome site!

  17. Tereza Avatar

    These look absolutely delicious! Will have to try these on the next baking sesh!

  18. Dede Avatar

    >>> Hi WM <<< These look Delish! i can't wait to make them but we are currently under kitchen construction and with out a stove – i'm wondering do you think these can be made some how in the microwave?? i don't know if i can wait until our stove works again to make these 🙂 Peace N <3

  19. Cristina Avatar

    Just wanted to say these were awesome. I first made them with homemade cinnamon apple sauce and it came out amazing! It’s also good with store bought, but hands down is better with homemade. It came out very moist, which has been difficult when baking paleo.

    1. Flemem Avatar

      No eggs in our house either – I usually sub 1 egg for 1T ground chia seeds mixed with 3T water (let it sit for about 3 min before you use). Before you do this I hope Katie can confirm if this will work:)

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