Pumpkin Chocolate Chip Muffins (Gluten Free)

5 from 25 votes
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These Healthy Pumpkin Chocolate Chip Muffins are supremely moist, naturally sweetened, and packed with pure pumpkin flavor. Prep a batch for the week, and enjoy these wholesome gluten free pumpkin muffins on repeat.Pumpkin chocolate chip muffins on a white board

In honor of the impending fall season (so close!), we’re eating gluten free Pumpkin Chocolate Chip Muffins on REPEAT. We’re actually eating and drinking pumpkin everything right now, because ’tis the season.

Think of this recipe as the love child between soft pumpkin pancakes and a piece of pumpkin bread. They’re supremely soft, melt-in-your-mouth moist, and naturally sweetened with maple syrup. 

These pumpkin muffins are perfect for breakfast on-the-go, a mid-day snack, or to satisfy a sweet tooth. And even though they taste decadent, they’re a nutritious option you can feel good enjoying regularly for breakfasts and snacks.

How to Make Pumpkin Chocolate Chip Muffins

These pumpkin muffins do not skimp on the pumpkin spice flavor. Just like with these Healthy Pumpkin Bars, every bite will wrap you up like a cozy plaid sweater on a chilly fall day.

They’re also SO easy to make, and require very little kitchen gadgets. So let’s get baking!

The Ingredients:Recipe ingredients in separate bowls on a gray surface with white labels

  • Pumpkin Puree: The flavor of canned pumpkin on its own is very mild, however it SHINES when mixed with spices! The pumpkin also helps make these muffins incredibly moist with using very little oil. Just be sure to look for pure pumpkin puree and NOT pumpkin pie filling.
  • Gluten Free Flour: Look for a gluten free all-purpose flour, such as this one by Bob’s Red Mill. GF flours can vary in ingredients, so be sure to use one that includes xanthan gum, which helps provide elasticity. (If you’re not making these muffins gluten free, you can just use regular all purpose flour.)
  • Eggs: You need two eggs to help provide structure to the muffins. I have NOT tried this recipe with flax eggs, so I cannot guarantee they will work.
  • Maple Syrup: In order to make these naturally sweetened, I use maple syrup in place of refined sugar. If you have not tried pairing pumpkin with maple syrup, it’s the ultimate fall treat! 
  • Oil: Very little oil is used in these muffins, and you can use any kind you have on hand. For example, vegetable, canola, melted coconut, or even olive oil.
  • Pumpkin Pie Spice: A must for quintessential fall flavor! This spice blend generally includes cinnamon, nutmeg, ginger, cloves, and sometimes allspice.
  • Mix-ins: I am a sucker for chocolate and pumpkin together, so I prefer these muffins with chocolate chips. Alternatively, toasted nuts such as pecans or walnuts, dried cranberries, or pumpkin seeds are all great options.
    • Dietary Note: If you need dairy free pumpkin muffins, be sure to use dairy-free chocolate chips, such as Enjoy Life brand, or swap the chocolate for a different mix-in.

Pumpkin muffins cut into on a white board

The Directions

Step 1: Combine Wet Ingredients

Preheat oven to 350ºF and line a 12-cup muffin tin with liners. Lightly coat liners with cooking spray.

In a large bowl, combine pumpkin puree, eggs, maple syrup, oil, and vanilla; whisk to combine.Eggs, pumpkin puree, maple syrup, and oil being whisked in a bowl

Step 2: Combine Dry Ingredients

In a separate smaller bowl, combine gluten free flour, pumpkin pie spice, baking soda, and salt; mix well to combine.Flour, spices, and baking power being whisked in a bowl

Step 3: Mix Wet and Dry

Pour dry ingredients into bowl with wet ingredients; whisk until smooth. Fold in chocolate chips.Dry ingredients being whisked into wet ingredients

Step 4: Divide into Muffin Tins

Divide batter evenly into prepared muffin tins, filling about two-thirds of the way full. If desired, sprinkle the tops with extra chocolate chips.Muffin batter being poured into muffin tins

Step 5: Bake!

Bake at 350ºF for 24 to 27 minutes, or until a toothpick inserted in the center comes out mostly clean.

Let cool in the muffin tin until cool enough to handle. Remove from muffin tin and let cool completely on a wire rack.One pumpkin muffin being displayed on a white board

Tips to Make this Recipe:

Use room temperature eggs

  • The secret to light and fluffy muffins is to make sure your wet ingredients are close to room temperature. This helps form a smooth batter that traps air and expands when heated in the oven. That expansion makes your muffins fluffy and light.

Use Quality Pumpkin Puree

  • Canned pumpkin can be a dicey adventure. In fact, most canned pumpkin isn’t pumpkin at all, but another variety of winter squash. I prefer using Libby’s pumpkin puree for the most consistent results and purest flavor.

Avoid Over-mixing the Batter

  • Even though we’re using gluten free flour, you still want to avoid over-mixing the batter. If the dough becomes too aerated, you end up with a gummy texture.

Pumpkin chocolate chip muffins being broke into to see texture

Storage Tips:

  • To Store. I suggest storing these pumpkin muffins in an airtight storage container or gallon-size zip-top bag for 4 days at room temperature. The pumpkin flavor becomes even more pronounced on day 2.
  • To Freeze. Freeze muffins in an airtight freezer-safe storage container for up to 3 months. Thaw and enjoy as desired (I like to individually wrap my muffins so I can grab them for quick breakfasts and snacks). 
    • To thaw, either let sit at room temperature overnight, or heat in the microwave using the “defrost” setting until warm.

More Healthy Ways to Bake with Pumpkin:

Healthy Pumpkin Barsreader favorite!

Mini Pumpkin-Tahini Cheesecakes

Brown Butter Pumpkin Tahini BarsFour Pumpkin Chocolate Chip Muffins lined up next to eachother

If you give these gluten free pumpkin muffins a try, snap a pic and tag #dishingouthealth on Instagram so I can see your beautiful creations. Also, follow along on Facebook and Pinterest for the latest recipe updates! I also really appreciate readers taking the time to leave a rating and review!

5 from 25 votes

Healthy Pumpkin Chocolate Chip Muffins

These Healthy Pumpkin Chocolate Chip Muffins are supremely moist, naturally sweetened, and packed with pure pumpkin flavor. Prep a batch for the week, and enjoy these wholesome muffins on repeat.
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 1 hour
Servings: 12

Equipment

  • Mixing bowls
  • 12-Cup Muffin Tin

Ingredients  

  • 1 cup canned pumpkin puree
  • 2 eggs, room temperature
  • 1/2 cup pure maple syrup
  • 1/4 cup oil (vegetable, canola, melted coconut, or light olive oil)
  • 1 tsp. vanilla extract
  • 1 cup gluten free all-purpose flour* (I recommend Bob's Red Mill 1-to-1 Gluten Free Baking Flour)
  • 2 tsp. pumpkin pie spice
  • 3/4 tsp. baking soda
  • 1/4 tsp. salt
  • 1 cup chocolate chips (I use Lily's brand)
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Instructions 

  • Preheat oven to 350ºF and line a 12-cup muffin tin with liners. Lightly coat liners with cooking spray.
  • In a large bowl, combine pumpkin puree, eggs, maple syrup, oil, and vanilla; whisk to combine.
  • In a separate smaller bowl, combine gluten free flour, pumpkin pie spice, baking soda, and salt; mix well to combine.
    Pour dry ingredients into bowl with wet ingredients; whisk until smooth. Fold in chocolate chips.
  • Divide batter evenly into prepared muffin tins, filling about two-thirds of the way full. If desired, sprinkle extra chocolate chips overtop.
    Bake at 350ºF for 24 to 27 minutes, or until a toothpick inserted in the center comes out mostly clean.
  • Let cool in the muffin pan until cool enough to handle. Remove from pan and let cool completely on a wire rack.

Notes

*My go-to gluten free baking flour is this one by Bob's Red Mill. GF flours can vary in ingredients, so be sure to use one that includes xanthan gum, which helps provide elasticity. 
*Nutrition facts calculated using Lily's baking chips.
  • To Store. I suggest storing these pumpkin muffins in an airtight storage container or gallon-size zip-top bag for 4 days at room temperature. The pumpkin flavor becomes even more pronounced on day 2.
  • To Freeze. Freeze muffins in an airtight freezer-safe storage container for up to 3 months. Thaw and enjoy as desired (I like to individually wrap my muffins so I can grab them for quick breakfasts and snacks).
    • To thaw, either let sit at room temperature overnight, or heat in the microwave using the "defrost" setting until warm.

Nutrition

Serving: 1muffin | Calories: 160kcal | Carbohydrates: 22g | Protein: 2g | Fat: 7g | Saturated Fat: 2g | Sodium: 105mg | Fiber: 2g | Sugar: 9g

I calculate these values by hand to ensure accuracy, however expect up to a 10% variable depending on food brands.

If you love this recipe, please leave a star rating and review below!

 

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24 Comments

  1. Say Tar says:

    5 stars
    I followed the recipe, no substitutions. Turned out amazingly delicious 😋
    Thank

  2. Christy says:

    5 stars
    Made them exact as recipe- texture and taste delicious- will make again

  3. Kelly Ann says:

    5 stars
    We love this recipe! They are a family favorite!

    1. Jamie Vespa says:

      I’m so glad the recipe was a hit! Thank you for taking the time to leave a review! – Jamie

  4. Catherine says:

    Can flaxmeal eggs be substituted for eggs due to an egg allergy. Will be using gluten free flour. Thank you for your reply.

    1. Barbara Martin says:

      5 stars
      Easy to make and a crowd pleaser-only had 1/4 cup chocolate chips so just sprinkled on top and worked out.

      1. Jamie Vespa says:

        I’m so glad the muffins were a hit, Barbara! Thank you for taking the time to leave a review!