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Gluten Free Chocolate Chip Muffins with Oat Flour

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These gluten-free chocolate chip muffins are made with oat flour for your perfect healthy breakfast option or even a mid-afternoon snack! Don’t let the word healthy fool you, because they are moist, fluffy, and will have your mouth watering!

Everyone who has a gluten intolerance or people who are looking for healthier alternatives when it comes to baked goods seem to have a hard time finding exactly what they are looking for. 

My version of chocolate chip muffins are not only gluten-free but are made with wholesome ingredients free of refined sugars and extra additives. 

Oat flour is a great gluten-free option for baking, especially when you don’t need your baked goods to rise. However, I have added some baking powder and baking soda to counteract that issue that we often run into when trying to bake with gluten-free flour. 

You will notice that I substituted coconut sugar for granulated sugar. But why? Coconut sugar actually has a significantly lower glycemic index when compared to table sugar. You can learn more about the benefits and differences between table sugar and coconut sugar from Livestrong.

Be sure to try my Peanut Butter Blondies, they are made with oat flour as well. Super healthy and delicious all wrapped into one bar.!

If you are a lover of all things chocolate, you HAVE to try my Peanut Butter Chocolate Banana Muffins! They have the perfect amount of chocolate and use whole ingredients, free of refined sugar! 

Ingredients for Gluten-Free Chocolate Chip Muffins 

Oat Flour – If you can’t find oat flour in your local markets, you can always make it from scratch by using gluten-free oats (any kind except the quick cook)

Coconut Sugar – You can substitute regular table sugar at a 1:1 ratio 

Baking Powder 

Baking Soda 


Coconut Oil – Some like to use applesauce instead, however, this will change the texture and may make the muffins a little drier. You can always try using half of the oil and use applesauce for the remaining. 


Greek Yogurt – using yogurt is not only healthier but keeps the muffins moist and contributes to them being fluffy

Vanilla Extract 

Mini Chocolate Chips 

You will also need a muffin pan, paper liners or reusable nonstick liners, mixing bowls, and a stand or hand mixer. 

Head over to my Amazon store to see my preferred baking ingredients and my other favorite kitchen gadgets! 

Storing Gluten Free Chocolate Chip Muffins 

Let the muffins cool in the pan for a few minutes then transfer them to a cooling rack to finish. Store in an airtight container or reusable bags up to 4-5 days. To keep them from getting soggy, line the bottom of your container with a paper towel, and keep one on top as well.

Can You Freeze Gluten Free Chocolate Chip Muffins?

Absolutely! Store a couple in each bag or food saver (if you vacuum seal) that way when you pull them out later you don’t have to eat all of them at one time or worry about them going bad. They will last for about 3 months, just to be on the safe side. Remember to label with dates! 

Let the muffins sit out at room temperature to thaw. Then reheat them in the microwave or air fryer to bring them back to the chocolatey goodness they were prior to freezing! 

I can’t wait to see what you have to say about my muffins! Be sure to tag me on Instagram after you make them! 

Here are some more muffin recipes you will fall in love with!

Vegan Sweet Potato Cinnamon Roll Muffins

Healthy Sweet Potato Banana muffins

Dairy-free Chocolate Banana Muffins

Vegan and Gluten-Free Gingerbread Muffins

PIN ME FOR LATERGluten-Free Chocolate Chip Muffins with Oat Flour

Gluten Free Chocolate Chip Muffins with Oat Flour

4.67 from 3 votes
Cook Time 22 mins
Total Time 22 mins
Servings 12 Muffins



  • Preheat oven to 350F degrees and line muffin pan with liners or spray the pan with nonstick cooking spray.
  • Combine sugar, baking powder and soda, salt, oil, eggs, vanilla, and yogurt. Stir until mixed.
  • Gradually add in the remaining ingredients, stir or mix well. Do not over mix your muffin batter!
  • Fold in chocolate chips.
  • Divide batter evenly into muffin cups.
  • Bake for 20-22 minutes.
Tried this recipe?Let us know how it was!

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  1. 5 stars
    Tried these while on a diet and they’re amazing! I substituted normal yogurt with vanilla coconut yogurt and used a banana instead of egg and they still come out perfect. You can add a little oat milk if the mixture is too dry.

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