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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. Samantha Avatar

    5 stars
    definitely include the vanilla extract! Made them without the first time. The second time I had it and it made a big difference! They are delicious, thank you for a simple, tasty, healthy recipe!

  2. Molly Avatar

    4 stars
    Hi, do these muffins need to be refrigerated if it takes a few days to eat them?
    My first batch turned out “okay”, they are somewhat taste-less so I think I need to look for sweetened applesauce or consider more add-ins. But, I put them in a container on the counter like I always do with baked goods and then I realized – these are mostly EGG, so I wonder if they are okay not being in the fridge?
    (When they are warm, the texture is very egg-cup-ish, but cold they are more muffin-like…)

  3. Alise Avatar

    Does anyone have any tips on how to make this more like a cake? I shared this recipe with a friend and she wants me to make her birthday cake from this. Also any tips on if I add diced apples? I plan on using a vanilla almond milk yogurt for a drizzle icing. Thanks!

  4. Andrea Avatar

    3 stars
    Mine only made 9 muffins and I used less than 1/3 per muffin. I thought cocounut flour seemed low for a muffin recipe.

  5. Rachel Tavroges-Hunter Avatar
    Rachel Tavroges-Hunter

    Hi! I’m based in the U.K. so please could you tell me measurements in grams / ml’s rather than cup size?

    Thanks so much!

  6. Mary Wilmot Avatar
    Mary Wilmot

    These were so good! I added the cocoa powder and chopped up apples and left out the sweetener and still soooo good. Even better with lots of butter on top 🙂 I can’t wait to try it in pancake form. These recipes are so easy and good and really make me feel like I can eat some of my favorite treats while paleo!

  7. Christa Avatar

    Hi! I was wondering if anyone has frozen these. I make them into mini muffins for my daughter but find that they can’t sit around for too long. Thoughts? Thanks!

    1. Mary Wilmot Avatar
      Mary Wilmot

      Yes! I have frozen them and then thaw them in the toaster oven. Works well!

  8. Anne S Avatar

    5 stars
    What muffin pans do you recommend? Mine always stick, and yours look so perfect!
    Thank you!

  9. Kim Avatar

    Turned out mushy, I added zucchini and Apple
    Also I tasted the baking soda quite a bit.

  10. Monika Avatar

    I tried your recipe today and it worked out great!
    But I’m wondering if you really use 2 – 3 TBSP of cinnamon. I am very very fond of cinnamon, but that even seems quite a lot to me. I mixed in 3 tsp and I think that’s just the perfect amount.
    Anyway, I love these Muffins! Thank you so much for sharing.

  11. Luda Avatar

    4 stars
    No allergies in our family. However i try to bake with coconut and almond flours off and on, especially for breakfast. My picky 4 children took a bite and only one approved it. To me these muffins taste good and i feel guilt free eating them.

  12. Sharon Avatar

    Hiya. Unfortunately mine turned out really eggy, not really what we expected for muffins. Double checked and did everything right. Or is that what they’re meant to taste like?

  13. Nayla Avatar

    These look amazing and I would love to try them, but I cannot find the ingredient list anywhere! Maybe it’s right in front of my eyes, but I just cannot find the ingredients. Am I the only one with this problem? Can someone please list them out for me?
    Thank you!

  14. Catherine Avatar

    5 stars
    Yes, that turned out to be totally correct. I made a recipe similar to yours ( The one on the back of the Nutiva coconut flour package) and used raw apple sauce in place of the liquids and sweeteners that were asked for. But I ended up using double the amount of coconut flour that you do. I think I also have one more egg in there. I was trying to get away from sweeteners but looks like it’s good you put just a little bit in. Using just raw applesauce turned out a bit bland but still yummy. I I used agave syrup in the last batch and that was way way too sweet.
    By the way, love your website!

  15. sarah Avatar

    5 stars
    My son & I loved these muffins! I halved the cinnamon and added cacao powder…yum what an Easter treat. Thanks Katie for another great recipe

  16. Irving Avatar

    5 stars
    Just made these and they turned out fantastic. I added a coconut sugar and chopped pecan topping. I also chopped up an apple I had sitting around and put it in the batter. Fantastic I will continue to make these in the future thanks!

  17. Patti Avatar

    5 stars
    I made these recently, and they’re delicious! I forgot to let the batter sit, but they turned out just fine. Great texture, nice & moist… YUM! I did add a little bit of walnuts and plan to try some other variations in the future. Thanks, Katie!

  18. Rachel Rivera Avatar
    Rachel Rivera

    I’m allergic to eggs. In 2 other baking recipes, I’ve tried doing a ground chia/water combo as a replacement, and the end result tasted so horrible, it was as if I was only eating chia bread or something. Is there someone who has tried this specific recipe with some kind or egg replacement? Would you be kind enough to post the measurements you used? I’m afraid to try chia/water in this recipe incase it ends up like the other recipes I’ve made, but if someone here says they tried it and the chia taste wasn’t overpowering, then I might give it a go. I’d hate to experiment with it again only to throw it all away 🙁

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