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Gluten Free Greek Yogurt Pumpkin Muffins

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These Greek Yogurt Pumpkin Muffins are the best fall snack! They are also gluten-free and can be made vegan-friendly! 

greek yogurt pumpkin muffin with a bite taken out sitting on small plate next to stack

We are in the season where if it’s not apples it’s pumpkin right? If you are been around here for any time at all you know I am a huge fan of pumpkin everything, but the recipes I make are simple, easy, and healthy when compared to your traditional holiday baking. 

gluten free pumpkin chocolate chip muffins stacked on top of each other

These greek yogurt pumpkin muffins are great for an easy breakfast, making in batches, a healthy snack, and even a delicious dessert! If there’s greek yogurt, I’m there! 

By the way, if you haven’t seen it yet, I just recently wrote a post for 22 Low Carb Pumpkin Recipes That Are Perfect for Fall that you just have to see! 

More Pumpkin Recipes I Promised You: 

Ingredients Needed for Greek Yogurt Pumpkin Muffins 

oat flour – if you don’t have oat flour you can make your own by grinding gluten free oats or swap it for almond flour instead.

Greek yogurt

Canned Pumpkin – make sure there are no added ingredients! 


coconut oil

maple syrup – you could also use honey

baking powder

baking soda


pumpkin spice


vanilla extract

dark chocolate chips – milk chocolate chips will work fine as well

How to Make Pumpkin Muffins with Greek Yogurt and That Are Gluten Free! 

Prepare your muffin tin by spraying it with non-stick cooking spray or place the paper liners in and preheat your oven to 425 degrees. 

In a mixing bowl, combine the flour, baking powder and soda, cinnamon, pumpkin spice, and salt. Stir together well. 

In a separate bowl, whisk the eggs together, mix in the pumpkin and greek yogurt then stir. Add in the maple syrup, coconut oil, and vanilla then mix until it’s combined. 

Add the dry ingredients into the bowl with the wet ingredients stirring well, but being careful not to overmix! 

Fold in the chocolate chips, saving some for the topping. 

Pour the batter into the muffin cups filling them ¾ of the way full. Sprinkle the remaining chocolate chips on top. 

Bake until you can stick a toothpick in and it comes out clean. It should take about 15 to 18 minutes. 

top shot of gluten free greek yogurt pumpkin muffins with chocolate chips before baking in the muffin tin

Before serving and removing the muffins from the pan, let them cool. 

Can These Be Made in a Vegan Version? 

Yes! You can swap the eggs and use flax eggs instead. For the greek yogurt, use a plant-based yogurt in its place.

pumpkin muffins on a wire rack after baking

Tips for Storing and Freezing 

Before putting the muffins in a container or Ziploc bag, make sure they have cooled completely. Store in the refrigerator due to the dairy. If you hate using plastic bags, I highly recommend you try Stasher bags! 

a few greek yogurt pumpkin muffins on a small white plate

If you want to freeze them after they have cooled put them in a freezer-safe container or bag and they will stay fresh for up to 2 months! 

To serve let them thaw at room temp or you can microwave them for a few seconds.

muffins stacked up on a small white plate

Now there’s nothing left to do but make the muffins and tag me on Instagram when you are finished so I can see what you think! 

More Easy Muffin Recipes Made with Whole Ingredients: 

muffins stacked up on a small white plate

Gluten Free Greek Yogurt Pumpkin Muffins

These Greek Yogurt Pumpkin Muffins are the best fall snack! They are also gluten-free and can be made vegan-friendly!
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Course Breakfast, Dessert, Snack
Cuisine American


  • 1 1/2 cups oat flour
  • 1 cup Greek yogurt
  • 1 cup 100% pumpkin canned
  • 2 large eggs
  • 1/4 cup coconut oil melted
  • 1/3 cup maple syrup
  • 2 tsp. baking powder
  • 1/2 tsp. baking soda
  • 1 tsp. cinnamon
  • 1/2 tsp. pumpkin spice
  • 1/2 tsp. salt
  • 1 tsp. vanilla extract
  • 1 cup dark chocolate chips 3/4 to mix in the batter and the rest for topping


  • Preheat the oven to 425° F and spray muffin tin with non-stick baking spray.
  • Add all of your dry ingredients to a bowl and mix until combined. In a separate bowl, add your wet ingredients. Add your dry ingredients to your wet ingredients and stir until combined. Do not overmix!
  • Fold in 3/4 cup chocolate chips.
  • Scoop batter into muffin tins filling about 3/4 of the way full. Sprinkle tops with the remaining chocolate chips.
  • Bake for 15-18 minutes or until you can stick a toothpick in a muffin and it comes out clean. Let cool for a few minutes and enjoy!
Tried this recipe?Let us know how it was!

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