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Healthy Apple Muffins– Gluten Free and Grain free

November 4, 2024 by Rachel S 5 Comments

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Moist, cinnamon-y, healthy apple muffins are a favorite fall treat for breakfast, snack, or even dessert! Gluten free, grain free, and refined-sugar free, these muffins are an easy recipe for everyday and delicious enough for a special treat.

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Muffins are a wonderful little treat now and then! Convenient to serve and pack, and tasty, these healthy apple muffins can work for gluten free, grain free, refined sugar free, and GAPS diet. You can also (easily) make them dairy free!

pin image for healthy apple muffins

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What makes these apple muffins healthy? Well, they aren’t perfect, but here are some benefits:

  • no refined sugar— most muffins recipes are loaded with sugar! They taste wonderful, but we may not feel so wonderful if we eat them often.
  • gluten free— not everyone needs to be gluten free, but more and more of us avoid gluten for different reasons.
  • grain free— many people do just fine with grains, especially fermented grains, but some of us feel much better without them. This is particularly true of anyone recovering from a chronic illness and working on gut health.
  • nothing highly processed— while the flours and coconut are somewhat processed, these healthy apple muffins are made with fairly whole foods. There isn’t anything unrecognizable or icky.

Is almond flour healthy?

While some tout almond flour as a health food, others avoid it like the plague! Who is right?!

Well, almonds have some problems. The hardest one to address is that almonds are fairly high in oxalates. Oxalates occur naturally in many foods (in varying amounts) and as waste produced in our bodies. They can contribute to many health problems, such as joint or other pain, urinary and thyroid problems, and kidney stones, among others. Read more here.

For anyone sensitive to oxalates, almonds may not be a good choice. Fermenting improves some downsides to almonds, but not oxalates. This is one reason I don’t bake with almond flour very often. Once in awhile seems to be OK; we don’t seem to be particularly sensitive to oxalates.

Fermenting Almond Flour

Though it won’t affect oxalate levels, fermenting almond flour can:

  • reduce naturally occurring phytic acid and enzyme inhibitors, which damage our guts
  • make it more digestible
  • improve the availability of the nutrients in almonds to our bodies
  • give baked goods a bit lighter texture– almond flour can lead to somewhat dense results, but fermented almond flour makes baked goods a little fluffier

Read more about almond flour fermenting here!

fermented almond flour in glass bowl on board

How to Ferment Almond Flour for Extra Healthy Apple Muffins

You don’t have to ferment the almond flour! If you tolerate almond flour well and normally bake with it without problems, feel free to skip the fermenting step. The recipe will work without it. You can make muffins on the spur of the moment with unfermented almond flour!

  1. Measure out your flour into a bowl. This recipe calls for 1 1/2 cups.
  2. Stir in kefir, whey, or yogurt so that the flour is coated and slightly moist. I used 1/4 cup of whey left from straining homemade yogurt. Other times I have used kefir. It won’t be very wet, but will look sort of crumbly. (In the picture, mine is a bit wetter than it should have been!)
  3. Cover and let sit at room temperature for a day or two. I prefer just one day. After two days, there is a stronger, yeastier flavor. Sometimes, I do half a day.
  4. If you don’t use your fermented flour right away, you can refrigerate it for up to a week, tightly covered. I always use it much sooner that that! It will ferment a bit more in the refrigerator, but not nearly as much as at room temperature.

While there is some planning involved in baking with fermented flour, it takes only a few minutes of hands-on time.

How to Make Healthy Apple Muffins

Once your almond flour is ready (whether you ferment or not), the steps are simple!

Mix all your dry ingredients– flour, baking soda, spices, salt– together. Thoroughly mix in the eggs, melted butter, honey and vanilla. The batter will be thin, but it will thicken somewhat in a couple of minutes. The reason for this is that coconut flour absorbs large amounts of liquid. It is nothing like other flours! Even though this recipe calls for just a little coconut flour, you will see a difference in the batter after a few minutes.

ingredients for healthy apple muffins

Peel your apple– usually just one is enough, but sometimes I use two if they are small. Grate it to equal 1 1/2 cups. This can be approximate! If you have a little more, it will be fine.

The apple lends flavor, of course, plus a lot of moisture. Besides that, the apple does a lot of the sweetening. I like to use a sweet apple, often Fuji, Gala, or Pink Lady, but you can use what you have.

grated apple on board

Stir the apple, coconut, and, optionally, chopped nuts into the batter. Portion it out into muffin cups and bake for 20 minutes or until done.

teal muffin pan with batter

Either remove your muffins as soon as they come out of the oven and cool them on a rack, or tip them so the air can circulate underneath them. Rule for life and muffin baking: keep your bottoms dry! These muffins are a little more prone to getting soggy because almond flour is kind of dense and all the apple and coconut affect the moisture.

healthy apple muffins in teal muffin pan

Can Healthy Apple Muffins be GAPS diet compliant?

Yes; if you are on the GAPS diet, pay attention to these details:

  • the almond and coconut flours should both be freshly ground
  • the almond flour should be fermented
  • if you include nuts, be sure you have soaked and dried them according to GAPS instructions
three healthy apple muffins on gray plate

Healthy Apple Muffins

Moist, cinnamon-y apple muffins are a favorite fall treat for breakfast, snack, or even dessert! Gluten free, grain free, and refined-sugar free, these muffins are an easy recipe for everyday and delicious enough for a special treat.
5 from 1 vote
Print Recipe Pin Recipe
Prep Time 15 minutes mins
Cook Time 20 minutes mins
Course Breakfast, Dessert, Snack
Cuisine American
Servings 12 muffins

Equipment

  • 1 muffin tin
  • 1 grater

Ingredients
  

  • 1 1/2 C almond flour Optionally fermented– see instructions below
  • 3 T coconut flour
  • 2 eggs or 4 egg whites
  • 1/2 C grass fed butter, melted
  • 1/4 C honey
  • 2 tsp ground cinnamon
  • 1 tsp ground nutmeg
  • 1 tsp baking soda
  • dash salt more if butter is unsalted
  • 2 tsp vanilla extract or vanilla powder or paste
  • 1 1/2 C peeled, grated apple about 1 apple
  • 2/3 C shredded coconut
  • 1/2 C chopped walnuts optional

Instructions
 

  • Preheat oven to 375° F. Line muffins tin with paper liners, if desired.
  • Peel and grate apple to equal 1 1/2 cups.
  • To almond flour, add coconut flour, honey, eggs, melted butter, cinnamon, nutmeg, vanilla, baking soda, and salt. Mix well until smooth. The mixture will thicken after a few minutes as the coconut flour absorbs liquid.
  • Stir in coconut flakes, shredded apple, and walnuts if using.
  • Scoop batter into muffin pan and bake about 20 minutes at 375° F until browned and a toothpick comes out with only a few crumbs.
  • Either remove muffins from pan to a rack or tilt them in the muffin pan so that the bottoms don't get soggy.

Notes

To Ferment the Almond Flour:
You don’t have to ferment the almond flour, but the muffins will be a little fluffier and a little better for you if you do. You can ferment for a few hours up to a couple of days. Here is what to do:
1. Measure out your 1 1/2 cups of almond flour.
2. Stir in about 1/4 C of cultured liquid. I used whey left over from straining homemade yogurt. Milk kefir works as well.
3. Cover and set at room temperature until you are ready to bake. If you don’t use the fermented flour in two days, put it in the refrigerator and use it within the week.
Keyword easy apple recipe, GAPS muffins, gluten free muffins, grain free muffins, healthy apple muffins

Make Healthy Apple Muffins Your Way!

  • for dairy free: sub coconut oil, lard, or other fat for the butter
  • try other spices– pumpkin pie spice, ginger, cardamon, clove– whatever you like!
  • skip the nuts, or use a different nut, such as pecans, or even seeds, such as pepitas or sunflower seeds
  • add raisins, currants, or dried cranberries or cherries
  • top with more nuts, streusel, or, after cooling, a glaze or frosting
  • while you are melting the butter, go ahead and brown it! Simply keep heating and stirring until the butter turns a bit tan and smells rich and warm, then turn off the heat quickly to avoid burning. Browned butter will deepen the flavor and make it more caramel-like. Delicious!
healthy apple muffins on gray plate

Looking for more muffins? Try these!

pumpkin bread with almond flour–make it as muffins!

pumpkin bread with coconut flour– bake in muffins cups

banana chocolate muffins with almond flour

banana chocolate muffins with coconut flour

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Filed Under: Breakfast, Desserts Tagged With: apple muffins, easy apple recipes, GAPS muffins, gluten free muffins, grain free muffins, healthy apple muffins

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Reader Interactions

Comments

  1. Rachel

    April 4, 2025 at 6:27 pm

    5 stars
    Cozy and yummy!

    Reply
  2. Annie

    November 7, 2024 at 10:22 pm

    These look so good! My husband can’t eat grain so I’m always looking for recipes like this for him. I’m saving this one!

    Reply
    • Rachel S

      November 8, 2024 at 10:39 am

      Yay! I hope he enjoys them!

      Reply
  3. Anonymous

    November 7, 2024 at 2:06 pm

    I’ve been looking for a good gluten free recipe for something sturdy enough to send overnight USPS to gluten free family for Christmas. This looks like the perfect option and I’m excited to make and gift these this year!

    Reply
    • Rachel S

      November 8, 2024 at 10:38 am

      I think they would stand up to shipping! Let me know how it turns out!

      Reply

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Happy Recipe Box

Welcome to Happy Recipe Box!

I’m Rachel. I share from-scratch recipes I have created for my family as we tweak our diet to  recover from health challenges. Join me in preparing flavorful, nourishing meals that don’t cost a fortune or take forever to prepare. Read more about me here.

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