Gluten Free Pumpkin Muffins With Chocolate Chips

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Fall in love with these tender and moist gluten free pumpkin muffins studded with chocolate chips.  The small batch recipe blends a flavorful oat flour blend, pumpkin puree, and all the best spices for fall.  Finish the lofty muffins with a sprinkle of cinnamon sugar for perfect breakfast muffins! 

Bite shot of a gluten free pumpkin muffin with chocolate chips stacked on another muffin.

Gluten Free Chocolate Chip Pumpkin Muffins

These gluten free pumpkin muffins capture all the fall breakfast vibes.  Adapted from my mini gluten free pumpkin bread recipe, the muffins are tall, soft, and saturated with delectable flavor.

And if you’re looking for more breakfast treats for fall, try my apple pumpkin streusel muffins, gluten free chocolate chip streusel muffins, apple spice bread, Hasselback baked apples, and the ever-popular cinnamon crunch pumpkin bread.

Why You’ll Love This Muffin Recipe

  • Tall muffins – The muffins bake tall with a delightful caramelized muffin top.
  • Flavorful oat flour blend – Oat flours gives the muffins a rich flavor.  My goal for all my gluten free recipes!
  • Moist muffins – The pumpkin puree combines with oil and brown sugar to yield super soft muffins that stay moist for days!
  • Flavored for fall – The two most iconic flavors for fall – pumpkin and pumpkin pie spice – shine in this recipe!
  • Loaded with chocolate chips – Every bite includes the texture surprise of mini chocolate chips!
Close up of a pretty chocolate chip pumpkin gluten free muffin on a cake stand.

Key Ingredients

  • Pumpkin Puree – Make sure it is pure pumpkin puree, not pumpkin pie filling.  The latter contains extra ingredients we don’t want or need.
  • Chocolate Chips – I like to use mini chips because they won’t sink to the bottom.  
  • Oat FlourAnthony’s sells my favorite oat flour.  You can also grind oats (certified gluten free!) to flour.
  • Sweet Rice Flour – Sweet rice flour provides extra structure to the muffins in the absence of gluten.
  • Tapioca Flour – Tapioca flour makes the muffins soft and tender.
  • Pumpkin Pie Spice – Use store-bought pumpkin pie spice to make your life easy!
  • Baking Powder – To give the muffins volume and make them tall.
  • Salt – Salt is key to balance and enhance flavors.
  • Brown Sugar – I use light brown sugar for flavor and moisture.  I recommend light because it does not have as much moisture content as dark brown sugar.
  • Granulated Sugar – My preference is organic cane sugar for flavor and less-processing.  Granulated white sugar will also work.
  • Coconut Oil – Melted refined coconut oil aid in keeping the muffins soft and moist.  You can try another neutral oil like canola or grapeseed.
  • Egg – 1 large egg to provide structure, texture, and moisture.
  • Vanilla Extract – For flavor!

Baking Tools

  • Mixing Bowls
  • Muffin Pan
  • Cookie Scoop

Tips For Successful Gluten Free Pumpkin Muffins

  • Grease the muffin wells completely – If you opt not to use cupcake liners, make sure you grease the wells of the muffin pan completely so the muffins won’t stick.
  • Mix the dry ingredients together first – Especially with a blend of flours, I like to mix them together first to ensure even distribution of all dry ingredients.  
  • It has to be pumpkin puree, not pumpkin pie filling – There are a lot of extra ingredients in the latter.  The only ingredient listed on the can should be pumpkin!
  • Let the batter rest before baking the muffins – Any batter will benefit from having a little time to rest.  The batter will hydrate and the flavors will develop so you end up with soft, perfectly muffin-dense muffins.  Otherwise, the muffins may be crumbly.
  • Use mini chocolate chips for better distribution – The mini chips suspend better in the batter because they are lighter.  
  • Cool completely before devouring – Gluten free baked goods always taste better when they have had a chance to cool.
Pretty interior of a gluten free pumpkin muffin full of chocolate chips on a stack of other muffins.

How To Make Gluten Free Pumpkin Muffins

  1. Preheat the oven to 350F degrees and grease you muffin pan – You can also use muffin liners, though for these pumpkin muffins, they will bake big and tall without.
  2. Whisk together all the dry ingredients – To make sure we don’t have lumps of a single ingredient!
  3. Mix the wet ingredients – I like to combine the sugars with the oil first to get the sugar fully saturated.
  4. Sprinkle the dry over the wet – And mix until no dry streaks remain.
  5. Let the batter rest! – For at least 5 minutes.  This will give the batter time to hydrate and flavors develop.
  6. Pour into the prepared muffin pan and finish with a couple extra chocolate chips and cinnamon sugar
  7. Bake for 22 minutes – Or until the tops and edges are golden and the muffins are springy to the touch.
  8. Cool in the pan for a few minutes, then cool completely on a wire cooling rack
Gluten free pumpkin muffins with chocolate chips arranged on a pretty white cake stand.

What To Make With The Leftover Can Of Pumpkin

You will have leftover pumpkin – regardless of the size of can you use.  Which may be a great thing so you can try other pumpkin recipes!

How Long Does Pumpkin Puree Last

  • Leftover pumpkin will last for about 1 week – Cover and refrigerate any leftover pumpkin puree if you intend to use it within a week.
  • Pumpkin puree can be frozen – Either put in a freezer-friendly covered container, or spoon into a freezer bag.  Freeze for up to 3 months and thaw in the refrigerator.


Can I use fresh pumpkin puree?

You can, though the fresh pumpkin may have a higher moisture content. You might want to blot the pumpkin with paper towel to remove any excess moisture.

Will a cup4cup gluten free flour work?

I don’t recommend it for this recipe. I find the cup4cup blends to be much drier than the flours I use.

What happens if I use dark brown sugar instead of light?

The muffins will still taste great! Though they may be slightly more dense because dark brown sugar has more moisture in it.

Can I use a different oil, instead of the coconut oil?

I recommend another neutral flavored oil like canola oil, grapeseed oil, or avocado oil.

How do I store leftover muffins?

The muffins can be stored covered at room temperature for up to 3 days. Or, you can freeze well-wrapped muffins for up to 3 months. Thaw at room temperature.

Two tall and moist gluten free pumpkin chocolate chip muffins stacked on top of eachother.

Gluten Free Pumpkin Chocolate Chip Muffins

Yield: 4 Muffins
Fall in love with these tender and moist gluten free pumpkin muffins studded with chocolate chips.  The small batch recipe blends a flavorful oat flour blend, pumpkin puree, and all the best spices for fall.  Finish the lofty muffins with a sprinkle of cinnamon sugar for perfect breakfast muffins! 
Prep10 minutes
Cook22 minutes
Total32 minutes




  • Preheat the oven to 350F degrees and adjust the oven rack to the middle position. Grease 4 wells of the muffin pan. You can also use cupcake liners.
  • In a small mixing bowl, whisk together the oat flour, sweet rice flour, tapioca flour, baking powder, salt, and pumpkin pie spice.
    6 tablespoons gluten free oat flour, ¼ cup sweet rice flour, 2 tablespoons tapioca flour, ½ teaspoon baking powder, ¼ teaspoon salt, 1 teaspoon pumpkin pie spice
  • In a medium mixing bowl, add the melted coconut oil and sugars. Whisk to combine. Then add the pumpkin, egg, and vanilla extract and whisk until smooth.
    2 tablespoons cold pressed refined coconut oil, melted, 3 tablespoons organic cane sugar, ⅓ cup pure canned pumpkin, 1 large egg, ½ teaspoon vanilla extract, ¼ cup light brown sugar
  • Sprinkle the dry ingredients over the wet ingredients and whisk until no dry streaks remain. Fold in the chocolate chips.
    ¼ cup mini chocolate chips
  • Let the batter rest for 5 minutes before baking. This allows the gluten free flours time to hydrate so the muffins bake tender and moist.
  • Pour the batter into the prepared pan. Sprinkle the cinnamon sugar over the top of the muffins. You can also dot a few more chocolate chips on top.
    2 to 3 teaspoons Cinnamon Sugar
  • Bake the muffins for 22 minutes, or until they are springy to the touch, a toothpick inserted in the middle comes out mostly clean, and the edges are golden.
  • Cool the muffins in the pan set on a wire cooling rack for at least 10 minutes. Then, using a sharp paring knife or offset spatula, gently go around the muffins to loosen them from the pan. Cool the muffins on the wire cooling rack completely. NoteI find gluten free baked goods taste better when they have had a chance to cool completely.
  • Store leftovers covered at room temperature for up to 3 days. Beyond that, the muffins may start to dry out. Well wrapped muffins can also be frozen for up to 3 months and thaw at room temperature.
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  • Pumpkin – Depending on the brand, canned pumpkin can have different names, but is the same thing:  Pumpkin Puree, Pure Pumpkin, 100% Pumpkin, Organic Pure Pumpkin.  Just be sure it is not Pumpkin Pie Filling
  • Leftover Pumpkin – You will have leftover pumpkin, regardless of the size can you use.  Check out my other pumpkin recipes to make another batch of pumpkin treats!
  • Serving Size – I have only tested this recipe as a small batch.  For doubling the recipe, I can’t say for certain how it would turn out, but if you try it, let me know!
  • Substitutions – The recipe has only been tested with the ingredients listed.  You could try to swap a Paleo flour blend 1:1.  However, I don’t recommend an all purpose gluten free 1:1 blend as I find it to be much drier.  The cane sugar can be swapped for white granulated sugar.
  • Brown Sugar – I recommend light brown sugar because dark may add too much moisture to the muffins and make them too dense.
  • Mini Chocolate Chips – I recommend mini chips to get more in each bite, and they won’t sink to the bottom.
  • Storing and Freezing – Store the muffins covered at room temperature for up to 3 days.  They can also be wrapped tightly in plastic wrap and placed in a ziploc bag, and frozen for up to 3 months.  Thaw at room temperature.
Course: Breakfast, Dessert, Snack
Cuisine: American
Author: Erin Cernich
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
About the author photo.

about the author ...

I'm Erin and I'm all about desserts - and a little bit of butter!

I've tested, written, and photographed hundreds of recipes on my website. Here you'll find the tastiest small batch gluten free and traditional desserts - all homemade, all simple, and all for you!

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