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    Home » Breakfast

    Gluten Free Pumpkin Chocolate Chip Muffins

    Updated: Sep 9, 2025 by Tiffany · This post may contain affiliate links · Leave a Comment.

     

     

    Jump to Recipe Print Recipe

    Fall is the ideal time of year for a batch of these gluten free pumpkin chocolate chip muffins.  They have the perfect moist texture and are filled with loads of melty chocolate chips and pumpkin spice.  

    This easy gluten-free muffin recipe will kick start your morning! They go perfectly with a cup of coffee for a breakfast on the go and make great lunch box snacks too.

    A batch of gluten free pumpkin chocolate chip muffins on a small cooling rack.

    This recipes only uses ¾ cup of pumpkin puree, so what will you make with the leftover pumpkin?  I recommend my gluten-free pumpkin muffins or this gluten free pumpkin bread recipe.  If neither of those sound good to you, check out this list of 32 ways to use leftover pumpkin puree.

    Jump to:
    • Ingredient Notes
    • Substitutions & Variations
    • How to Make Gluten-Free Pumpkin Chocolate Chip Muffins
    • Expert Tip
    • Storage
    • More pumpkin recipes to try:
    • Recipe

    Ingredient Notes

    These delicious pumpkin muffins require just a handful of simple ingredients that can be found in any grocery store.  They are both gluten free and dairy free as written.

    Ingredients for gluten free pumpkin chocolate chip muffins sitting on a marble counter.
    • Gluten-Free Flour Blend - I use Bob's Red Mill 1-to-1 Flour Blend for this recipe.  You can use the gluten free flour blend of your choice, but ensure it contains xanthan gum or a similar binder.  I don't recommend a single flour replacement, like almond flour or coconut flour - those won't work here.  
    • Pumpkin Pie Spice - Since pumpkin itself has a rather mild flavor, most of the flavor we associate with pumpkin comes from this spice mix.  
    • Pumpkin Puree - Make sure you use pure pumpkin puree, not pumpkin pie filling which contains sugar and other ingredients.  You can use canned pumpkin puree or homemade, although I do find homemade to have more moisture. If you decide to use homemade pumpkin puree, I would recommend omitting the added milk from the recipe.
    • Dairy-Free Chocolate Chips - I used the Enjoy Life mini chocolate chips.  I think mini chips work great in muffins because they are more evenly spread throughout every bite.  You can use your favorite brand - and trying white chocolate chips would also be delicious!

    See recipe card for full ingredient list and quantities.

    Substitutions & Variations

    • Not Dairy Free - Use dairy milk in the same measure.
    • Make it Vegan - I have not tried this recipe with an egg substitute.  With just a single egg in a very moist muffin, you might be able to just omit the egg.  The other option would be to use flax eggs.
    • Chocolate Switchup - Replace the chocolate chips with dairy free white chocolate chips.  The combination tastes like pumpkin pie topped with whipped cream. YUM!
    • Add some crunch - Add in ½ cup of chopped nuts or pumpkin seeds.  I think pecans would be a great choice in this recipe.
    • Make Mini Muffins - Divide the batter into 24 mini muffins.  The baking temperature will be the same, but the cook time will be about 5 minutes less.

    How to Make Gluten-Free Pumpkin Chocolate Chip Muffins

    All of my gluten-free muffins and quickbread recipes are made using the muffin method.  No mixer is required.  Everything is done with two bowls, a whisk and a spatula. 

    This easy recipe makes approximately eight muffins.  Although I've shown a 6-cup muffin tin in the photos, you will need to line a 12-cup pan with eight muffin liners. Follow the baking instructions to the letter to get nice a nice tall muffin top!

    Dry ingredients combined in a large mixing bowl.

    STEP 1: Combine the gluten free flour, baking powder, pumpkin pie spice, salt, and sugar in a large mixing bowl.  Whisk well to mix.

    An egg beaten in a small bowl.

    STEP 2: Crack the egg into a medium bowl and whisk it until it's frothy like soap bubbles.

    Pumpkin puree, oil, vanilla, and milk added to the bowl with the beaten egg.

    STEP 3: Add the pumpkin puree, oil, milk and vanilla extract to the bowl with the beaten egg. Whisk together until smooth.

    Wet ingredients being mixed into the bowl of dry ingredients.

    STEP 4: Pour the wet ingredients
    into the bowl with the dry ingredients.  Fold together with a rubber spatula for about 10 strokes.

    Mini chocolate chips added to the pumpkin muffin batter.

    STEP 5: Add the chocolate chips to the pumpkin muffin batter.  Fold together about 5 more strokes until they are evenly distributed.

    Unbaked pumpkin chocolate chip muffins in a baking tin sitting on a marble counter.

    STEP 6: Portion the muffin batter into your prepared muffin pan.  I like to use an ice cream scoop to make it easy! Sprinkle a few extra chocolate chips on top and dust with coarse sugar.  Now you're ready to bake!

    Expert Tip

    To check your muffins are done, gently poke the top of the muffins with your finger.  If the top springs right back, the muffins are fully baked.  If it leaves and indentation, bake for another 2 minutes and check again.

    Freshly baked pumpkin chocolate chip muffins in a metal pan.

    Storage

    Allow the muffins to cool for 10 minutes in the pan, then remove them to cool completely on a wire rack.  

    Once the muffins are room temperature, you can store them in an airtight container in the refrigerator for up to 4 days.  I like to reheat for 15-20 seconds before serving. 

    These muffins will also freeze well.  Wait until they are completely cooled, then wrap them individually in plastic wrap and place inside a freezer bag.  You can store them up to 3 months.  

    A batch of gluten free pumpkin chocolate chip muffins cooling on a wire rack.

    More pumpkin recipes to try:

    • A slice of pumpkin coffee cake served on a white plate.
      Pumpkin Coffee Cake
    • A pumpkin banana muffin with a bite taken out.
      Pumpkin Banana Muffins
    • A stack of gluten free pancakes on a white plate.
      Gluten Free Pumpkin Pancakes
    • A stack of three gluten free pumpkin waffles on a serving plate.
      Gluten Free Pumpkin Waffles

    If you try this recipe, please leave a 🌟🌟🌟🌟🌟 star rating and let me know how you liked it in the comments below.

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    Recipe

    Several gluten free pumpkin chocolate chip muffins on a cooling rack.

    Gluten Free Pumpkin Chocolate Chip Muffins

    These delicious gluten free pumpkin chocolate chip muffins are the perfect breakfast treat for Fall! They are tender and moist with loads of chocolate chips and pumpkin spice.
    Author: Tiffany
    5 from 1 vote
    Print Pin Rate
    Course: Breakfast
    Cuisine: American
    Prep Time: 10 minutes minutes
    Cook Time: 27 minutes minutes
    Total Time: 37 minutes minutes
    Servings: 8
    Calories: 251kcal
    Prevent your screen from going dark

    Ingredients

    • 1 Cup Gluten Free 1-to-1 Flour Blend I use Bob's Red Mill
    • 1 teaspoon Baking Powder
    • ¼ teaspoon Salt
    • ½ teaspoon Pumpkin Pie Spice
    • ⅔ Cup Sugar
    • 1 Egg
    • ¾ Cup Pumpkin Puree not pumpkin pie filling
    • 3 Tablespoons Oil
    • 2 Tablespoons Non Dairy Milk omit for homemade pumpkin puree
    • ½ teaspoon Vanilla
    • ½ Cup Mini Chocolate Chips
    • 2 Tablespoons Turbinado Sugar optional
    US Customary - Metric

    Instructions

    • Preheat oven to 400 °F (204 °C) degrees. Line 8 muffin cups with paper liners.
    • In a large bowl, combine flour, baking powder, salt, pumpkin pie spice, and sugar. Whisk together well and set aside.
      1 Cup Gluten Free 1-to-1 Flour Blend, 1 teaspoon Baking Powder, ¼ teaspoon Salt, ½ teaspoon Pumpkin Pie Spice, ⅔ Cup Sugar
    • In a second bowl, whisk the egg until frothy.
      1 Egg
    • Add the pumpkin puree, oil, milk, and vanilla to the beaten egg. Whisk together until smooth.
      ¾ Cup Pumpkin Puree, 3 Tablespoons Oil, 2 Tablespoons Non Dairy Milk, ½ teaspoon Vanilla
    • Pour the wet ingredients into the bowl with the dry ingredients. Fold together about 10 strokes until combined.
    • Fold in the chocolate chips, reserving about 1 tablespoon for topping the muffins.
      ½ Cup Mini Chocolate Chips
    • Scoop the batter into the prepared muffin tin. Fill the cups to the top. Sprinkle the tops with the remaining chocolate chips and the coarse sugar. Allow the muffins to rest for 10 minutes before baking.
    • Bake in preheated oven for 5 minutes. Reduce temperature to 350 °F (177 °C) degrees and cook an additional 20-22 minutes until the tops spring back when gently poked.
    • Remove from oven and cool in the pan for 10 minutes. Then transfer the muffins to a wire rack to cool.

    Notes

    STORAGE: Allow muffins to cool completely before storing.  Place them in an airtight container lined with a paper towel on the bottom.  Store in the refrigerator for up to 4 days.
    Calories: 251kcal | Carbohydrates: 41g | Protein: 3g | Fat: 9g | Saturated Fat: 2g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 4g | Trans Fat: 0.04g | Cholesterol: 22mg | Sodium: 129mg | Potassium: 63mg | Fiber: 3g | Sugar: 28g | Vitamin A: 3697IU | Vitamin C: 1mg | Calcium: 59mg | Iron: 1mg
    Tried this recipe?Mention @wellfedbaker or tag #wellfedbaker!
    Tiffany

    Tiffany is the recipe developer, stylist and food photographer behind Well Fed Baker. As a lifelong baker who had to go gluten free and dairy free in 2016, Tiffany strives to share allergen friendly recipes that never feel like they are free from anything.

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    Hey, I'm Tiffany!

    I love sharing gluten-free comfort food and homestyle baking, featuring Dutch oven meals, nostalgic dinners, classic baked goods, with dairy-free or allergen-friendly options. My recipes lean Southern, seasonal, and practical.

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