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!

Gluten-Free Apple Cinnamon Breakfast Muffins

Renee -
Preserve your apples, and send the kids off to school with healthy gluten-free apple cinnamon breakfast muffins!
5 from 23 votes
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast
Cuisine American
Servings 12 muffins


  • 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.
Keyword gluten-free apple muffin recipe, gluten-free apple muffins, gluten-free muffin recipe
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Recipe Rating


  1. 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?

    1. 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 🙂

  2. 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)

    1. 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?

  3. 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!

  4. 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.

  5. 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!!!)

  6. 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.

  7. 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!

  8. 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!

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