Gluten-Free Apple Muffins – Almond & Coconut Flour

These easy gluten-free apple muffins contain yogurt and fresh apple chunks for a soft texture. Naturally sweetened with honey, juicy apple bits, and plump raisins, these apple cinnamon muffins are a nutritious snack, Paleo-friendly, and made with grain-free flours.

October 31, 2025

cinnamon gluten-free apple muffins in a basket

Cinnamon Apple Muffins - Grain Free

Gluten-Free Apple Muffins are perfect for a delicious breakfast or a healthy snack that will keep you energized between meals. With just the right amount of cinnamon, these muffins feature chunks of apple and yogurt, creating a sweet, tender texture. You won’t even notice that they are gluten-free! The whole family will love these delightful baked goods.

What are the Best Apples For Baking?

The chart above outlines the best apples for baking muffins, cakes, pies, and cobbler/crisps. For this gluten-free apple cinnamon muffin recipe, I love combining Granny Smith with other apples on the chart. If it’s apple season, you may find local growers at the market, which is always a bonus for superior taste and peak nutritional value. Using two apples in the easy muffin recipe creates a sweet-tart flavor profile. If you are using one apple, use a crisp, not-too-sweet variety. This article from Nielsen-Massey includes additional information on using apples for baking, snacking, and freezing.  

Clean ingredients used in gluten-free apple muffins recipe

Apple Muffin Ingredients and Notes

  • Butter: unsalted, works best. If using salted butter, reduce the salt by 50%.
  • Apples: I like one Granny Smith and one crisp, sweet-tart red apple. See the chart above for varieties. 
  • Almond flour: Use blanched almonds; whole ground almond flour (skins included) is grainier.
  • Coconut flour, or unsweetened shredded coconut flakes, absorbs a lot of moisture. I use a small amount in the batter because of the apple juice. I don’t want to dry the apples with a towel and lose the precious flavor. I found, through experimentation, that coconut flour or flakes yield the same results as drying the fruit. Coconut flour will give a smoother texture than coconut flakes, which provide a little crunch. If you don’t use coconut, the muffins may be too wet in the middle.
  • Cinnamon – this recipe calls for quite a bit, 1 Tablespoon + 1 teaspoon – not a typo!
  • Ginger Powder: for spicy warmth.
  • Raw, local honey: contains beneficial compounds and provides a moist texture and tight crumb to the muffins. If consumed at room temperature (not baked), local honey may help alleviate seasonal allergies.  
  • Plain unsweetened yogurt: no sugar; (homemade if following SCD).
  • Raisins: – I love using golden raisins, but regular ones are great too.
  • Cupcake liners: Paper or foil work.

Preparing Apples for Muffins

core and slice apples for gluten-free muffins

1

Core and slice apples.

shred and chop apples for cinnamon apple gluten-free muffins

2

Use a box grater to shred half of the apple slices and a paring knife to chop into bite-sized chunks.

shred apples with food processor for muffins

3

Or use a food processor with the coarse shredding blade.

How to Grate Fruit for Apple Cinnamon Muffins

I like to have a combo of shredded and chunky apples in the muffins. It gives the muffins a wonderful, moist, and fluffy texture. First, core and slice apples with an apple corer. Do not peel them. Shred half the apple wedges and dice the other half into chunks. If using a food processor, use the coarse shredding blade rather than the fine shredding blade. If using a box grater, use the coarse-shred side as well, being careful not to nick your knuckles. When the apple wedges become too small to grate, set them aside and cut them into bite-sized pieces. 

Equipment Needed

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Gluten-free apple muffins in a baking tin
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More Reason to Love Gluten-Free Apple Muffins

  • These portable make-ahead snacks are freezer-friendly. Cool and freeze in lidded containers for up to 3 months; Great for grab & go snacks, from freezer to the lunchbox.
  • If you have an apple tree, are lucky enough to have a friend with one, or like to visit the local orchard in the fall, this recipe is handy.
  • Great snack when detoxing from processed foods.
  • Fantastic gift idea: box up these delightful baking goods for a homemade treat everyone will appreciate.
  • Specific Carbohydrate Diet (SCD) friendly; if you are on an elimination diet of grains or processed sugar, these SCD muffins are a lifesaver. 
  • Budget Recipe: Homemade snacks are always less expensive than buying them from the store. In less than 45 minutes, you have a dozen family-friendly muffins!

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Gluten-Free Apple Muffins – Almond & Coconut Flour

5 Stars 4 Stars 3 Stars 2 Stars 1 Star

5 from 3 reviews

Gluten-Free Apple Muffins with warm, spicy cinnamon and ginger make a delicious breakfast or a healthy midday snack that will keep you energized between meals. The chunks of apple and yogurt create a sweet, tender texture, and you won’t even notice that these moist apple cinnamon muffins are gluten-free. The whole family will love these delightful baked goods!

  • Author: Karen
  • Prep Time: 15
  • Cook Time: 25
  • Total Time: 40
  • Yield: 12 1x
  • Category: Breakfast
  • Method: Baking
  • Cuisine: Classic
  • Diet: Gluten Free

Ingredients

Units Scale
  • 1/4 cup unsalted butter, melted
  • 2 small apples, grated with some bite-size chunks (2 cups). I like one Granny Smith and one crisp, sweet-tart red apple. See the photo in the post.
  • 2 cups almond flour
  • 1/4 cup coconut flour or unsweetened shredded coconut
  • 1 teaspoon baking soda
  • 1/4 teaspoon salt
  • 1 teaspoon ground ginger
  • 1 Tablespoon + 1 teaspoon cinnamon
  • 2 eggs, beaten
  • 1/3 cup raw honey
  • 2/3 cup plain unsweetened yogurt can be Greek or plant-based; (homemade if following SCD)
  • 1 teaspoon vanilla
  • 1/3 cup raisins. I prefer golden; any raisin will do.
  • 12 – 15 cupcake liners – paper or foil

Instructions

  1. Preheat the oven to 350º. Line a 12-count muffin pan with cupcake liners—paper or foil.
  2. Melt the butter: Cut the butter into four pieces and place it in a microwave-safe dish with a handle. Cover with a paper towel, silicone lid, or parchment paper. Cook on medium heat for 60 seconds. Pull out and stir. Repeat in 5 -10-second intervals, as needed. Let the butter cool slightly while combining the other ingredients.
  3. Prepare apples: I like a mix of shredded and chunky apples in the muffins. It gives the muffins a wonderful, moist, and fluffy texture. First, core and slice apples with an apple corer. Do not peel them. Shred half the apple wedges and dice the other half into chunks. If using a food processor, use the coarse shredding blade rather than the fine shredding blade. If using a box grater, use the coarse-shred side as well, being careful not to nick your knuckles. When the apple wedges become too small to grate, set them aside and cut them into bite-sized pieces. See the illustration in the post above.
  4. Combine Dry Ingredients: Add almond flour, coconut flour or flakes, baking soda, salt, and cinnamon to a large bowl. Whisk to combine.
  5. Combine Wet Ingredients: Add beaten eggs, yogurt, honey, melted butter, and vanilla to a medium bowl. Stir to mix everything. Add wet ingredients to the large bowl with the dry ingredients. Stir gently to combine. Don’t overmix.
  6. Fold: in raisins and apple pieces.
  7. Spoon batter into liners, filling them to the top. Turn oven temperature to 350º F (180 º C) and bake for 22 – 25 minutes.
  8. Cool muffins for 10 minutes, then remove them to a cooling rack. This allows the muffins to continue baking for a bit. If your muffins are a little overdone, remove them to a cooling rack as soon as they are cool enough to handle.
  9. Store Muffins: after cooling, store muffins in a lidded container for 4 days at room temperature, 1 week in the refrigerator, or 3 months in the freezer.

 

Notes

Variations:

  1. Use apple pie spice, which varies by brand and includes cinnamon, nutmeg, allspice, ginger, cardamom, and cloves.
  2. Use currants instead of golden raisins.

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Let me know your thoughts on this post!

7 responses to “Gluten-Free Apple Muffins – Almond & Coconut Flour”

      • What a beautiful way to bless a new mama — this absolutely warmed my heart. 💛 Thanks for informing me and readers that many of the ingredients help nursing moms with milk production. I’ll add this feature to the recipe. Thank you for sharing your doula wisdom.

  1. Delicious and easy to make. The apple chunks are so good. They are not too sweet like baked goods from the store.

  2. So delicious and easy, perfect to have on hand for a healthy but quick grab and go breakfast or snack.

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Karen the Supper Sanity Home Chef

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Supper Sanity

Hello, I’m Karen, a very passionate meal planner! As a mother of three, I have been planning family menus for years. When I was diagnosed with a digestive condition, I found it necessary to follow an eating regimen that eliminated many ingredients. Meal planning became a health necessity. I’ve learned a lot and want to share my resources to simplify meal planning, shop efficiently, and cook affordable homemade meals. If you wish to try new recipes, plan healthier meals, and enjoy a great dinner with your friends and family, Supper Sanity can help.

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