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These Healthy Apple Muffins are made with oat flour and are packed with seasonal apples and raisins. These gluten free apple muffins are easy to make, using just one bowl to put together! They make a great on-the-go breakfast or snack, will be a hit with picky kids and are 100% nut-free!

Healthy Apple Muffins with Oats and Raisins

These Healthy Apple Muffins are made with oat flour and coconut flour and are stuffed with shredded apples, cinnamon and raisins. They are the perfect fall breakfast that is happens to be nut-free, gluten-free and refined sugar free! These kid-friendly muffins are easy to make (and a fun baking project with the kids) and because they are nut-free they are safe to send to school. Keep a batch in the freezer and pop in the lunch box in the morning and these healthy oat muffins will be ready to go by the time lunch time hits. They are also a healthy midday snack that truly everyone will love!

Ingredients for Apple Oat Muffins

Scroll down for the full recipe!

  • Oat Flour
  • Coconut Flour
  • Unsweetened Apple Sauce
  • Maple Syrup
  • Butter or Coconut Oil
  • Apples
  • Raisins
  • Cinnamon
  • Baking Powder
  • Eggs

What kind of oat flour is best to use?

As we’ve said in previous oat flour recipes, we recommend you buy premade oat flour. It isn’t expensive and it is easy to purchase in most stores. However, if you want to make your own oat flour, you certainly can. We just recommend you try to get it as fine as possible.

How do you measure oat flour

If you have an electronic kitchen scale at home, it’s best to use it here to measure oat flour. Oat flour can be tricky to measure as it can be easily compacted, even straight from the bag. The same goes for coconut flour because such a small difference in measuring it can impact a recipe because it is an absorbent flour. So we’ve included the weight in grams here. Any electronic kitchen scale can switch between grams and ounces, and grams are more precise so we’re offering that. If you don’t have a scale: lightly packing the oat flour into the cup measurement gets you as close to the correct measurement as possible. For coconut flour scoop it in the tablespoon and then level it off.

To Peel or Not to Peel the Apple

The apples are grated before being folded into the batter. Grating the apples both adds moisture to the muffin and makes sure that the apples are cooked through quickly. You can leave the peel on the apple, or you can peel it off. We prefer the texture and nutritional value that leaving the (organic) peel on imparts, but feel free to remove it if you prefer.

How to store Healthy Apple Oatmeal Muffins

We’ve tested storing these at room temperature covered loosely, in an air tight container and in the freezer. They all work! But we prefer to keep these at room temperature covered (in a non-air tight way) for two days at most. The muffins get more moist as the days go on, especially in an airtight container, which can make them feel dense.

So if you want to keep them the freshest, you can store in the freezer. If you are packing these for lunches for kids, or a snack for yourself, you can take them from the freezer the morning of and place in a container. In an hour or two the muffins are defrosted and ready to eat.

If you like this healthy apple recipe, check out these others:

If you like this muffin recipe, check out these others:

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Gluten Free Apple Muffins

5 from 9 votes
These Healthy Apple Muffins are made with oats and are packed with seasonal apples and raisins. These gluten free apple muffins are easy to make, using just one bowl to put together! They make a great on-the-go breakfast or snack, will be a hit with picky kids and are 100% nut-free!
Servings 12
Prep Time 10 minutes
Cook Time 18 minutes
Total Time 28 minutes


  • 2 large eggs
  • 1/2 cup unsweetened apple sauce
  • ½ cup grass-fed butter or coconut oil melted and slightly cooled
  • ½ cup maple syrup
  • 1-1/2 cups 180g oat flour
  • 2 tablespoon 14g coconut flour
  • 2 teaspoon baking powder
  • ½ teaspoon cinnamon
  • 1/4 teaspoon salt
  • ½ cup raisins
  • 2 medium apples grated (about 1-1/2 cups lightly packed grated apple)


  • Preheat oven to 350ºF and line a 12 cup muffin tin with silicone or parchment paper liners.
  • In a large bowl add eggs, apple sauce, melted butter and maple syrup and whisk together. 
  • Add oat flour, coconut flour, baking powder, cinnamon and salt and mix with a spatula until smooth.
  • Fold in raisins and apples.
  • Fill each muffin cup ¾ full.
  • Bake in the middle rack for 18-20 minutes, or until the muffins spring back when touched.


We’ve found store bought oat flour to be different than homemade. We prefer the texture to store bought and suggest that is what you use.
If you have an electronic scale at home please use it to measure the flour, as these flours are notorious for being difficult to measure with cup measurements.
If your oat flour or coconut flour is very clumpy sift them.


Serving: 1cupcakeCalories: 106kcalCarbohydrates: 17.9gProtein: 1.6gFat: 3.8gSaturated Fat: 1.5gCholesterol: 32mgSodium: 106mgFiber: 1.2gSugar: 15.9g
Course: Breakfast
Cuisine: Dairy-free, Gluten-free, Nut-free
Author: Lexi

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  1. Hi,
    I’m new to your site. I made these and my neighbor loved them. I however can’t have honey or maple syrup. Is there anything else I can use for sweetner. No sugar for me.
    Thanks in advance for any help you can give me.
    Great recipe

  2. The instructions say to add salt in with the flours and other dry ingredients. I don’t see salt in the ingredients. How much salt would you suggest?
    Making these right now. They look good

  3. I think this paleo muffin might actually work for me b/c even if the middle sinks slightly, you can’t tell b/c it’s topped with lots of yummy goodness 😀

  4. These are gorgeous and look so crumb-y and sweet! I love the way you did the apple ribbons on top! (Just a note, you included the “nut-free” sticker at the top, but these little babies do have nuts!)

  5. These look amazing Lexi! So perfect for the holiday (or anytime around). Shana Tova to you and your family!

  6. These are fantastic!!! I had a feeling it was almond flour used, but couldn’t tell because they don’t have an overpowering nutty flavor like some Paleo baked goods. Thanks for sharing some with me. Now I need a few apples so I can make them at home. 🙂