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Gluten Free Apple Cinnamon Breakfast Muffins

September 29, 2018

Preserve your apples, and send the kids off to school with healthy gluten free apple cinnamon breakfast muffins!

My toughest transition….

Apple season is just about one of the only ways you can drag me kicking and screaming out summer and into the autumn equinox. I know some of you live for all your pumpkin spice, wool mittens, and cozy blankets, but this beach bum has a hard time saying good bye to her flip flops and hello to fuzzy boots. Last weekend we celebrated the autumn equinox with our first apple picking of the season, and we couldn’t have asked for better fall apple picking weather, or any better of a farm experience!

A new organic apple farm favorite!

We were lucky enough to get a chance to visit Evergreen Lane Farm & Creamery, a “new to us” organic apple farm, one their first day of their apple picking season. There trees were simply gorgeous boasting a variety of apples to choose from, including Ida Reds and Jonagolds, which is what we picked! There were buckets of bruised or dropped apples near their goats and horses that the girls had a riot feeding to the animals. It was such a fun day trip, and felt so good to show the girls the importance of supporting farmers that care for their plants and land in a way that is sustainable and safe.

A bushel of fun!

We brought home a bushel of apples, and my goodness have we had some fun with our apples this week! I did end up making some apple baked oatmeal right off the bat, and then the girls and I settled in at my Instant Pot to pump out quart after quart of delicious “Kid Prep” applesauce for the freezer. When I was down to my last 5 pounds of apples, I decided to create a new muffin for school mornings, and we are so in love with these fluffy, delicious apple cinnamon muffins.

High muffin standards…

Because if I’m going to be sending my girls off to school fueled on a muffin, they are going to have to make it through my checklist! Our household has to be gluten free, but I also want the ingredients “count.” Which means I want balanced macro-nutrients in the muffin. These muffins have a great balance of protein, satiating friendly fat, and energy fueling good carbohydrates. They also happen to taste and feel amazing, which is also on my checklist, because that does matter!

How to make these work on a school morning!

  • Get all of the dry ingredients into a small bowl so you can dump them into the wet ingredients super quick in the morning.
  • Have the muffin tin ready to go the night before. Line the muffin tin with either silicone muffin cups or unbleached paper liners.
  • You can measure out the oil and coconut sugar right into the mixing bowl the night before as well. Then, in the morning, all you have to do is add the eggs to beat, and all the rest of the ingredients go in after that while the oven is pre-heating.
  • Use an apple cutter and your food processor to make the apples easy to manage. It literally takes less than a minute to cut 2-3 apples with your apple cutter, and then just buzz them up in the processor quick instead of hand chopping to save time.

Freezer friendly?

Yes! That actually happens to be one of my criteria for a “keeper” on my muffin list. If I can stick the leftover muffins in the freezer, or make a double batch to stock up my freezer and preserve the apples, then I’m totally in! And these muffins definitely fill that need. Having freezer muffins make for easy grab and go school morning breakfast or lunchbox additions.

A note on ingredients and swaps

Please know that it is impossible for me to test out every possible ingredient swap. I noted some alternative swaps in the recipe. Any unanswered questions you can drop comments at the bottom of this post, and I will try my best to help!

Print Recipe
5 from 23 votes

Gluten-Free Apple Cinnamon Breakfast Muffins

Preserve your apples, and send the kids off to school with healthy gluten-free apple cinnamon breakfast muffins!
Prep Time10 minutes
Cook Time20 minutes
Total Time30 minutes
Course: Breakfast
Cuisine: American
Keyword: gluten-free apple muffin recipe, gluten-free apple muffins, gluten-free muffin recipe
Servings: 12 muffins
Author: Renee -


  • 4 eggs I haven’t tried egg free, but I would imagine flax eggs or applesauce “eggs” would work – the muffins will probably not puff up as much but they would still taste great.
  • 1/3 cup coconut sugar Raw honey or pure maple syrup would work too. If you have older kids used to sweeter things, I would bump this up to ½ cup. As is these muffins have a mild sweetness, perfect for a healthy breakfast muffin for little ones.
  • ¼ cup olive oil or melted coconut oil or butter
  • 2 tsp vanilla extract
  • ¼ cup coconut milk or raw milk/yogurt if you tolerate dairy
  • 1 cup cassava flour
  • ½ cup blanched almond flour If you are nut free, you could try more cassava flour
  • ½ cup tapioca starch
  • 1 tbsp cinnamon
  • 1 tsp aluminum free baking powder
  • 1 tsp baking soda
  • ½ tsp sea salt
  • 2 cups chopped apples it ended up being 2-3 small apples for me – I just buzz them up in the food processor quick for the chop


  • Pre-heat the oven to 350 degrees and line your muffin tin with silicone muffin cups or unbleached paper cups.
  • Beat the eggs, coconut sugar, and olive oil for 1 minute until frothy.
  • Add the rest of the ingredients, blend to combine, and then fold in the apples.
  • Scoop the muffin batter into your lined muffin tin (recipe makes 12 large muffins), and bake at 350 degrees for 20 minutes. A toothpick should come out clean if they are done. Let the muffins cool 5 minutes before transferring to a cooling rack to cool completely. To store leftovers in the freezer, let the muffins cool completely, wrap them up in plastic or beeswax wrap, and then into a freezer bag.

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  • Reply Katherine Reimer September 30, 2018 at 6:57 am

    I’d love to make these with einkorn! I wonder how I could do that? I don’t know if I could just sub all the flours. Any suggestions off the top of your head?

    • Reply Renee Kohley October 3, 2018 at 11:04 am

      Hi Katherine! Since we have to be gluten free, I am really unfamiliar with how einkorn bakes. I’m sorry that doesn’t help you much! I’m sure it would work – maybe look at the batter in the photo and try to match that consistency 🙂

  • Reply Sara September 30, 2018 at 11:22 am

    We are a gluten free house but not necessarily paleo….can I swap the cassava flour and tapioca starch for the King Arthur gluten free all purpose flour? (While still including the almond flour)

    • Reply Renee Kohley October 3, 2018 at 11:05 am

      Hi Sara! I have not tried that yet, but it should work. It may not be an equal swap though. Maybe follow the consistency of the batter in the photo and that will help?

  • Reply Tessa Simpson October 1, 2018 at 1:42 pm

    5 stars
    Gosh darn these look So good! I love chunks of apple IN the muffin, fall goodness!

  • Reply Emily @ Recipes to Nourish October 1, 2018 at 6:07 pm

    5 stars
    The texture of these is so perfect! I love the apple cinnamon flavor, so lovely for this time of the year. Looks like you had a wonderful time apple picking, how fun!

  • Reply Jean October 1, 2018 at 7:34 pm

    5 stars
    I can just imagine eating one of these on a crisp chilly morning with a cup of coffee. Sounds like heaven! Love how you can actually see the apple chunks.

  • Reply Megan Stevens October 1, 2018 at 7:47 pm

    5 stars
    Yay on the macronutrients: These look perfect and terrific!! We love muffins so much in this home, and I can’t wait to make these! (BTW, me too~ so hard to let summer go!!!)

  • Reply Yang October 1, 2018 at 9:56 pm

    5 stars
    Ahhh, apples and cinnamon, these muffins make me love fall so much! <3

  • Reply Lindsey Dietz October 2, 2018 at 9:32 am

    5 stars
    What perfect muffin tops you have (and I mean that in the BEST possible way!). Also, the memories of your girls picking apples… priceless!

  • Reply Irena Macri October 2, 2018 at 9:50 am

    These look so good! I love apple inside muffins and cakes, it reminds me of childhood because my grandma always baked with apples and pears. Would love to try these.

  • Reply Joni Gomes October 2, 2018 at 10:40 am

    5 stars
    Yes to apple season and these muffins! So easy, so nutritious and yum!

  • Reply Katja October 2, 2018 at 3:31 pm

    5 stars
    Mmmmmmm… I just made these, and they are SO tasty. I’m trying to use cassava flour more. Great recipe!

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  • Reply Raia Todd October 4, 2018 at 2:43 pm

    5 stars
    My kids would love these! And love that they can be made with honey, too. 🙂

  • Reply Kelly @ A Girl Worth Saving October 5, 2018 at 11:54 am

    I love that you went a picked apples for this and then made this recipe. It makes the recipe even more special for you and your girls!

  • Reply Karen @ Seasonal Cravings October 5, 2018 at 2:46 pm

    5 stars
    I can’t think of a better breakfast for my kids before starting the school day. Wonder if my daughter could make these on her own. I’ll bet so!

  • Reply ChihYu Smith October 5, 2018 at 9:28 pm

    5 stars
    Apple flavored muffins are the best!!

  • Reply Anne Lawton October 6, 2018 at 3:38 pm

    5 stars
    These muffins sound so good, just perfect for all of the apples that are in season now.

  • Reply Cristina Curp October 7, 2018 at 8:13 pm

    5 stars
    Yes! We have been getting so many apples in our CSA box! This recipe is perfect 🙂

  • Reply STACEY CRAWFORD October 8, 2018 at 2:00 am

    5 stars
    These apple muffins are so yummy and I love how the photos are styled and shot with a lovely rustic Fall theme.

  • Reply Kari - Get Inspired Everyday! October 8, 2018 at 9:21 am

    5 stars
    These look so perfect! I have loads of apples right now and apple cinnamon is too good to beat!

  • Reply Carol Little R.H. @studiobotanica October 8, 2018 at 1:35 pm

    5 stars
    Thanks for sharing your apple stories.. I need to get hold of that apple sauce recipe too.
    I can’t wait to try these muffins. Love your recipes!

  • Reply Tonja October 19, 2018 at 1:34 pm

    5 stars
    Didn’t have tapioca flour so I used honey for the sweetener (1/3 cup was more than enough!) and 1 1/4 cups of cassava flour then the almond flour.. worked out great!

    • Reply Renee Kohley October 24, 2018 at 10:04 am

      Good to Know Tonja! Thank you for sharing!

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  • Reply Mariana August 13, 2019 at 12:14 pm

    Hi Renee, thanks for such amazing recipes! My kids love everything I’ve cooked from you. Is there any substitute for the tapioca starch? I wasn’t able to find it. Thanks!

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      Hi Mariana! I’m not sure – did you look for tapioca flour – they are the same thing and sometimes that is how it is labeled!

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  • Reply Erin September 15, 2019 at 2:43 pm

    You’re so lucky to live near an organic apple orchard! We don’t have anything around here. And those muffins look fantastic!

    • Reply Renee Kohley September 22, 2019 at 8:47 am

      Thank you Erin! Yes, I know they are hard to come by! We are very blessed!

  • Reply Raia Todd September 30, 2019 at 10:57 am

    5 stars
    These look perfect! I love a good muffin for breakfast… or snack.

  • Reply Daniela Modesto October 1, 2019 at 9:13 am

    5 stars
    Gorgeous and delicious! I love starting my day with a sweet breakfast and coffee!

  • Reply Kristen Wood October 1, 2019 at 4:47 pm

    5 stars
    These sound utterly delicious! I’m certain my kids would love them, too. 🙂

  • Reply Dana Currie October 1, 2019 at 11:16 pm

    I’m wondering, because my family isn’t gluten free, could I substitute sprouted whole wheat flour? If so, what quantity would you suggest?

    • Reply Renee Kohley January 14, 2020 at 11:24 am

      Hi Dana! I’m sure that would work, however I am not sure on the amount! I can’t have wheat so I am not familiar with how it swaps!

  • Reply Don Baiocchi October 4, 2019 at 2:49 pm

    5 stars
    Now these are some perfect-looking muffins! I love how simple they are to make, too.

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    oh, I love the idea of olive oil in these! That mild fruity flavor mixed with apples is amazing!!

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    Oh, my! These look so good! Perfect for those busy school mornings, and I can still have my son have a great start to his day!

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