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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. charms Avatar

    can you use butter in place of the coconut oil? are they generally good substitutes fir each other?

  2. Syvella Avatar

    I just finish making this recipe. However, I didn’t make muffins I made it as a bread. 🙂
    I only use one 1 tablespoons of cinnamon and I added some raisins, I used Truiva for my sweetener and it taste so DARN GOOD! I think I am going to add some almond milk next time and cook them as pancakes and see how they come out!

  3. Lauren Trussell Avatar
    Lauren Trussell

    I made the muffins and added some fresh blueberries. They turned out very well, but for some reason they did a number on my stomach. I’ve been having one for breakfast with some berries and they keep me full, but the tummy ache is not a good side effect. Any idea what would cause this? I followed the recipe exactly, just added the blueberries.

    1. Wellness Mama Avatar
      Wellness Mama

      Have you eaten them before without the blueberries without problem? For some people, the large amount of fiber can cause stomach issues the first few times you eat it.

      1. Lauren Trussell Avatar
        Lauren Trussell

        No, this is the first time I made them. I eat blueberries often, though. Would the large amount of fiber still cause trouble even though my diet includes tons of veggies and some fruit daily? Thank you for your help. I enjoyed the taste of the muffins, but they’ve given me a “fat” feeling and lots of tummy trouble 🙁 If I can figure out the glitch, I want to keep baking them!

        1. Wellness Mama Avatar
          Wellness Mama

          The fiber could still be the problem, as it has a lot more than even most vegetables. It could also mean you are intolerant to coconut though… do you eat other coconut products without problem? Maybe
          try them again in a few weeks and see how you do? If you see a reaction several times in a row though, I’d avoid them..

          1. Lauren Trussell Avatar
            Lauren Trussell

            Ok, that sounds like a plan. I do eat other coconut products (like roasted veggies in coconut oil) and use coconut oil on my skin, so I don’t think I have an intolerance. I’ll try them again and maybe give some of the batch away to friends. That way I’ll eat only a couple instead of one each day for several days 🙂 I so appreciate your help!

          2. Heidi Avatar

            Sometimes when we mix fruit with other types of foods, it can create gas and other problems. I am one of those people who cannot tolerate mixing…. : /

    2. Joan Avatar

      I found that adding a lot of cinnamon upsets my digestive track. I am going to try allspice next time.

  4. Elizabeth Avatar

    hi 🙂 is there any way of making these in advance – either the night before or on a bake day and freezing them? how well do they keep in a tin or do they go all soggy? many thanks 🙂

    1. Angela Avatar

      Hi, I can tell you that these freeze really well; I’ve been baking a batch, freezing them on the same day and getting them out as needed for the kids’ breakfast.

  5. Colleen Santiago-Sprister Avatar
    Colleen Santiago-Sprister

    we have an abundance of zucchini & squash from our garden right now and wanted to make muffins with them to freeze… have you ever done that with the coconut flour and adapting this recipe??  Do you think it would work?

  6. Sara Adams Avatar
    Sara Adams

    Sounds good.  I just made an apple spice muffin with coconut flour the other day but used diced apples.  I wonder if the kids would like this one better. 

  7. Cecilia Powers Avatar
    Cecilia Powers

    where do you get your coconut flour? and what is a good price for it? i’m excited to try this out!

    1. Wellness Mama Avatar
      Wellness Mama

      I get from Tropical Traditions, but you can find it at some grocery
      stores and even on Amazon, sometimes for cheaper.

      1. Alisha Avatar

        Hi, I am addicted to your website, really great stuff! I am wondering if you have ever tried to make your own coconut flour? It is pretty expensive so I was thinking of trying this, with the coconut chips maybe.

        1. Elysia Avatar

          I’m all for DIY but coconut flour is one of the few things I wouldn’t make myself. There’d be no way you could get it fine enough because it’s so fiberous. And apparently coconut flour is not ground dried coconut. I’m able to find it for less than $5/pound and since you use such a small amount in each recipe it lasts for a long time.

          I’ve tried a couple different brands, and each brand is not equal. Bob’s Red Mill is coarser ground and leads to a very fiberous-textured baked good. The Coconut Secret I use now is a little finer. I bought it cheap on Swanson Vitamins. I also have a bag of Nutiva from Azure Standard so we’ll see how it compares.

          Happy baking!

          1. Melody Avatar

            What did you think of Nutiva? I’m new to gluten free baking and I don’t care for it.aybe I’m just not familiar with the texture. I’m wondering if I should try the Coconut Secret.

    2. Elie Avatar

      I buy Nutiva coconut flour off of amazon in a 3 pound bag. You can also find it on iHerb.com or Vitacost.com has it in 1 pound bags.

      1. Chaloh Avatar

        FYI…my local Costco has the 3-pound bags of Nutiva coconut flour for $6.99 🙂

  8. Karen Avatar

    FYI: I also just made these directly from the recipe as a “bread” in an 8×8 glass pan. I just baked it a little longer until it was browner on the sides and not sticky on the top. Less to clean up! 🙂

    1. Wellness Mama Avatar
      Wellness Mama

      Great idea and good to know it works! I’ll have to try that too!

      1. CJ Avatar

        Worked out GREAT! This is now my go-to bread. 🙂 I tried a different recipe today and it failed miserably. Your recipe is FOOL PROOF and Delicious!!!

    2. CJK Avatar

      I did the same in an 8×8 glass pan. The bread came out so nice, you can slice a piece in half and use like regular bread for sandwiches! Going to try it without the cinnamon and use em for PBJ, etc… Super texture!

  9. Karen Avatar

    Almond flour works well! I melted the coconut oil. This recipe is going in my weekly rotation! Thanks Wellness Mama!

  10. Karen Avatar

    The muffins (for me) took about 20 minutes. Also, I highly recomend using the cocoa powder as an extra engredient!

  11. Sam Thomason Avatar
    Sam Thomason

    These sound great, but Im wondering, does anyone know the rough calorie count and other nutrition information. I swear, if I make something labeled “healthy” my husband thinks that means he can eat double to balance it out 🙂 Thanks!

    1. Wellness Mama Avatar
      Wellness Mama

      They are low in carbs and high in protein, so he will probably find
      he gets full before be can overeat them! If weight loss is a concern,
      these shouldn’t raise blood sugar enough to cause weight gain.

      1. Jayne Avatar

        Thank you! Does anyone have a carb count? I am diabetic and need to count these.

    1. Wellness Mama Avatar
      Wellness Mama

      I haven’t yet… I’m hoping to be able to buy some almond flour
      really soon. I’d think you’d have to adjust it some, since almond
      flour acts a little more like wheat flour, and coconut flour is much
      more dry. I’d think you’d have to add closer to 3/4 or 1 cup, but as
      long as the consistency is right, it should work.

    2. Hoy Avatar

      I did this morning.  Cut the eggs down to three, and ended up tripling the flour (1.5 c) as the almond flour is not nearly as dry.  I also added a tsp. of cider vinegar to activate the soda.  Only 1.5 tbsp of oil just to cut back.  They were marvelous and with company over didn’t make it past noon 😉

      1. Rainah Ness Avatar
        Rainah Ness

        5 stars
        I wondered if I was the only one thinking about vinegar in response to the baking soda. Thanks for posting your experience! I’m looking forward to doing the same!

  12. Abby Avatar

    Delicious!!! And great texture too! I didn’t have any applesauce, so I used my food processor to shred two medium apples. Then switched to the blade attachment and added everything else and blended it all together. I think the apples make them sweet enough I didn’t even need to add any honey! Can’t wait to try a banana nut version next….

  13. Julia Benson Avatar
    Julia Benson

    Love. Love. Love this recipe. Just made my second batch of the week. Satisfies the craving for sweet and bready! I miss Panera bagels!!!

        1. Beatriz Avatar

          I have been makingg these for some time now and yes, definitely only 4 eggs is better. Otherwise it is too eggy

      1. Melissa Avatar

        I agree. I made them one time and they smelled delicious so I couldn’t wait to try them. We all took a bite and looked at each other. Almost everyone was sure that I left something out because they tasted terrible. I may try them again with less egg and maybe some honey added in?

  14. Audrey 'Huss' Charba Avatar
    Audrey ‘Huss’ Charba

    I’m going to try this in the morning. Do you make raw or cooked applesauce? I’m wondering if my raw applesauce will have too much moisture…

    1. Wellness Mama Avatar
      Wellness Mama

      I’ve always just used my homemade canned applesauce, so I’m not sure.
      Raw applesauce may have too much moisture, but you may be able to
      just use a little more coconut flour or a little less applesauce. The
      consistency you are going for is thicker than pancake batter but
      thinner than peanut butter. I used a small measuring cup to scoop
      into the muffin tins. I would think as long as you can get the
      consistency right, it should work.

      1. Shelly Avatar

        I hope someone can give me some pointers. I didn’t know where else to ask for help. I have a traditional mini pumpkin chocolate chip muffin that my son just loves. He has given up wheat with us, but this is one he is missing. How do I go about adapting or changing it to make it healthy?

        1. Wellness Mama Avatar
          Wellness Mama

          You could sub pureed pumpkin for the applesauce in this recipe, add pumpkin pie spices to taste and chocolate chips, and it should be somewhat similar.

        2. Kris Avatar

          Elana’s pantry has lots of grain free recipes. I have gotten a good pumpkin one there if you don’t find one here.

        3. Belle Avatar

          Try part oat flour and part brown rice flour in your recipe. I make pumpkin cranberry muffins with brown rice flour.

        4. Mari Avatar

          4 stars
          I substituted almond meal for some of the coconut flour. And I cut out an egg and added 1 tablespoon flaxseed meat mixed with a little water for added omega 3’s and fiber.

        5. Tammie Wright Avatar
          Tammie Wright

          5 stars
          You can throw oats in the blender & turn it into flour. I make banana chocolate chip muffins with it. My recipe uses 2 cups. Add in a tsp. of xanthum gum for stickiness since there’s no gluten.

    1. Wellness Mama Avatar
      Wellness Mama

      As long as coconut oil is not hydrogenated and is in cold pressed,
      extra virgin, unfiltered form, it actually has a good effect on
      cholesterol. The medium chain fatty acids and lauric acid are great
      for the body and don’t raise cholesterol at all. check out this
      article if you are interested in reading more: https://wellnessmama.com/5734/coconut-oil/

      1. Samantha Avatar

        1 star
        This is the first recipe from your book I made . Measured carefully and double checked all ingredients. Definitely only made 9 muffins! I even put a little less than one-third cup in each. Kind of disappointed

      1. Jody Avatar

        Not ALL and ANY carbs raise cholesterol. It’s the bad carbs, aka the simple carbs that can raise cholesterol. Complex carbs can actually lower cholesterol. What else raises cholesterol? Animal protein (if eaten too often). I suggest reading the fabulous and research based book called “The China Study” by Colin Campbell. It’s so informative.

        1. Patty Avatar

          The recipe calls for tablespoons of cinnamon, is that right? Anyone think that it was too much? Love cinnamon but would love feedback on that before trying.

    2. Josh Gitalis Avatar
      Josh Gitalis

      Coconut oil has no cholesterol. Cholesterol is something that only animals make, thus it’s only in animal foods and animal products. In addition, the idea that cholesterol is bad for us, has been disproven.

    3. Jason Avatar

      Coconut oil has zero cholesterol, not that it matters anyway. After more than a decade of research confirming that dietary cholesterol intake does not contribute to blood cholesterol levels, the world health organization finally acknowledge the same. Coconut oil is high in a healthy type of saturated fat called medium chain triglycerides. It is not only a healthier alternative to other oils, but actually a fat that you should try to intentionally get in your diet.

  15. Julia Benson Avatar
    Julia Benson

    I tried this recipe tonight! Pretty tasty and much better than the attempt I made using an incomplete recipe from elsewhere on your site last night!

  16. Allison Avatar

    Those sound so yummy! One question – do you melt the coconut oil before mixing it in?

      1. Kaye Avatar

        Thank you for that clarification! I get confused with some of the baking recipes and never know to melt or not to melt!

      2. Danielle anderson Avatar
        Danielle anderson

        5 stars
        I mixed everything on low in my Vitamix, made it super easy to pour into muffin tins as well.

    1. Dawn MH. Avatar
      Dawn MH.

      That was the same question I had too! It was unclear if you needed to melt or measure at solid. ALSO…. It says to use an immersion blender or whisk but I am guessing I can do this with a hand mixer as well??

  17. Michelle Avatar

    These look wonderful, I can’t wait to try them out! I’ve been making wheat blueberry muffins lately, but I like the idea of using coconut flour and coconut oil even more!

4.23 from 170 votes (89 ratings without comment)

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