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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. Irene Avatar

    It was a hit I lightly sprinkled a little organic confectioners sugar on top & all 3 Lil ones gobbled them right up with some almond milk! Thx again;) the teen is a different story lol 😉

  2. Irene Avatar

    Thx Katie… I feel like your my friend! A definite lifesaver in this abrupt (for health reasons)& awesome lifestyle change to Paleo – we aren’t aren’t all the way there but we are getting there!!! I’m a mom of four who didn’t know where to start & though I’ve been on quiet a few other sites this is my go to! I’ve tried quite a few of your recipe & tonight is apple cinnamon night! My kiddies & I love the choc donut holes & we had your version of chipolte the other night!!! Can’t wait to see if they love these! But I already think they will smells great ! Thank you Thank you Thank you !!!!

  3. Yvette Missri Avatar
    Yvette Missri

    These sound amazing and I can’t wait to try them! Thank you! Question though – I can’t eat eggs (though my kiddos and hubby can) – would replacing the eggs with chia seeds ruin the high protein/nutrition profile of the recipe? If so, I can just make it for them of course, but wanted to get your thoughts. Thank you!

  4. nimvin Avatar

    Just tried this recipe – Followed it to the letter with the following exceptions: I used 1/2 cup of butter instead of coconut oil, added about 1 cup of chopped nuts, and used 2 Tbs of Xylitol instead of the honey. It made 6 standard muffins and 1/2 dozen mini muffins. They are not very sweet with the Xylitol, but I find that pleasing. They came out beautifully!! This is a very easy recipe and the results are excellent! I’m adding it to my “go to” recipe file. The ONLY thing I would change is to add a teaspoon of salt, as it did seem to need the savor. Other than that – WONDERFUL RESULTS!! Thank you VERY much for this recipe. I am going to try it as a loaf next time and maybe use it as a sandwich bread.

  5. Valerie Avatar

    Tried this today and my hubby loved it. He’s the gluten free one. I did change a few things. 1. 5 eggs. I can’t imagine putting five eggs in anything. His cholesterol level is inching up as it is, combined with coconut oil, and I thought it might just burst. I subtracted 2 eggs. 2. I put the amount of applesauce in and apple pieces. 3. I also added dried mulberries to them. Once baked, it added a toffee like flavour to them. 4. And for flavour, in addition to the cinnamon, I added 1/2 tsp of nutmeg and allspice. 5. I did a cinnamon, nutmeg, brown sugar crumble for the topping.
    Made quite a few changes and they were amazing! Thanks for the inspiration.

  6. Captured by Jess Avatar
    Captured by Jess

    Is the 2T of honey meant to go IN the muffins or as the drizzle part?

  7. Jessica Rech Avatar
    Jessica Rech

    I use locally purchased duck eggs, they’re bigger than chicken eggs so I was worried about the 1/2 cup coconut flour being able to handle all the liquid. But it did beautifully! I never thought it could be so absorbent!

  8. Jamie Avatar

    I substituted the applesauce with pumpkin and added pumpkin spices. They were gross; don’t try it :P. I tried to salvage them with glaze, but no one would eat them. The texture is really off too. I’m hoping the apple would be better. I can’t imagine there being enough sweetness in just the apples; maybe if I added raisins? I’m trying to think of a way to put the ones I made in some other dish so all that food won’t be wasted.

  9. Kit GearhartSchinske Avatar
    Kit GearhartSchinske

    I just made these today with diced apple and nuts added. I greased the muffin tin with coconut oil, but the muffins still stuck to the bottom of the pan. Any suggestions for preventing this? Thanks.

  10. elise Avatar

    i just want to make 5 muffins, can i just cut the ingredient measurements in half?

  11. Kim Wojcuilewicz Avatar
    Kim Wojcuilewicz

    This is exactly what I was looking for to make a yummy homemade school snack for my son (and the younger ones, too!). Going to bake them right now! Thanks!! 🙂

    1. Kim Wojcuilewicz Avatar
      Kim Wojcuilewicz

      SUCCESS!! I’m not a huge fan of the flavor (I think I’ll add in a banana and some apple chunks next time!) the texture is AMAZING! I tried one and thought “there’s no way the kids will like this” Well I was wrong! They asked me for them and then asked for more! Score! Thanks for such an easy recipe that my kids love!! 🙂

  12. Kelli Avatar

    I’m new to coconut flour and the whole idea of GF in general. Are these muffins GF?

  13. Sherri Jackson Avatar
    Sherri Jackson

    Hi- When I printed out the recipe, the name of the recipe did not appear at the top; Just thought you would want to know this.

  14. Jas Koh Avatar

    You mentioned that extra virgin coconut oil will lower cholesterol.

    1) Is extra virgin coconut oil = cold pressed coconut oil?

    2) can we use the extra virgin or cold pressed coconut oil for frying?

    3) I currently use a coconut oil that says, “Neutral Flavor” on the bottle, mainly for frying as someone once told me that extra vigin or cold pressed coconut oil should not be used for frying. I assume this neutral flavored coconut oil is neither extra virgin nor cold pressed. Is it safe for frying?


    1. Wellness Mama Avatar
      Wellness Mama

      Organic extra virgin coconut oil is cold processed and is a stable saturated fat that can be used at high temperatures…

  15. Jas Koh Avatar

    I do not have an oven. Would it be possible to steam the muffin instead of bake?

  16. Emily Avatar

    Wait, I need to make … say… 50 muffins. What’s the serving amount for the one you posted? I’m a new muffin making machine and need advice.

    1. Wellness Mama Avatar
      Wellness Mama

      The one posted will make 10-12, but I”d make in small batches to make sure things mix evenly…

  17. Racheal Lewing Avatar
    Racheal Lewing

    I just made these today for my son’s first birthday. I added the cocoa powder, vanilla, and honey in with the batter. I also made a date paste “icing” with vanilla, a little extra honey, and cocoa powder. I baked them in large muffin pans for about 22 minutes. They ended up being moist, but lacked flavor. Next time I’ll only use 1/2 cup applesauce and add 1/2 cup butter in addition to adding additional honey or date paste for additional sweetness. These are definitely worth making again, just with a few adjustments. Thanks for the recipe!

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