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Home » Blog » Recipes » Desserts » Pumpkin Chocolate Chip Muffins (Paleo, Gluten Free)

Pumpkin Chocolate Chip Muffins (Paleo, Gluten Free)

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Craving tasty and healthy pumpkin chocolate chip muffins that also happen to be paleo and gluten-free? These honey-sweetened almond flour pumpkin muffins can be made ahead and kept in the freezer so you can easily heat one up when pumpkin spice blend season hits!A dozen pumpkin chocolate chip muffins are on a wire rack. The red banner on top has the Nom Nom Paleo logo of a cartoon girl with pigtails. The red label at the bottom says that the recipe is paleo, gluten free, and grain free.

Moist pumpkin chocolate chip muffins (hey—“moist” as an adjective isn’t cringey when it’s the desired texture for food) are perfect for fall weather or whenever you want to transport yourself to that cozy autumnal time of year.

Similar to my other pumpkin-y paleo desserts, this one’s super-easy to make—and you won’t even need to source any hard to find ingredients.

Useful Baking Tips!

Seasoned bakers and pastry chefs always recommend that folks use a kitchen scale to measure ingredients when making baked goods because there can be up to a 20% difference in the amount of flour depending on how it is measured. And let’s face it: baking requires increased accuracy because small changes in volume can result in suboptimal treats.

Pouring almond flour in a large silver bowl on top of a digital kitchen scale to make paleo pumpkin chocolate chip muffins.

Use a kitchen scale

For all of my baking recipes where precision in calculating ingredient amounts is critical, I always add metric measurements so you can weigh each component on a kitchen scale for consistency. Need another reason to use a kitchen scale? Cleanup is faster because you won’t mess up a bunch of measuring cups and spoons. Just tare (or zero out) the scale in between measuring ingredients. I use this kitchen scale to make everything from these pumpkin chocolate chip muffins to paleo potstickers!

Work quickly

As soon as the dry and wet ingredients are combined in this pumpkin chocolate chip muffin recipe, you must work quickly because the baking soda has been activated. If you dawdle, your muffins won’t rise as well in the oven!

What are some paleo-friendly chocolate chip brands?

These days, you can find paleo-approved (i.e., dairy-free, refined sugar-free, junk free) chocolate chips or bars pretty easily online or at the grocery store. Some brands I like include Hu Gems, Guittard Mindful Choices, and Eating Evolved. But here’s a dirty little secret: I don’t always use paleo chocolate in my recipes—I just choose a dark chocolate bar or chips (70% cacao or higher to keep the sugar level low) that I like to eat!

Can you substitute other ingredients?

Not to sound like a broken record player or anything, but once again, I’m no paleo baking expert, so I DON’T KNOW. I’m not sure if you can use an egg substitute or use another flour in place of almond flour in this pumpkin chocolate chip muffin recipe because I haven’t tried out all the different possible permutations. But if you have success with any ingredient substitutions, please let us all know in the comments section below!

How do you store and reheat pumpkin chocolate chip muffins?

You can freeze any pumpkin chocolate chip muffins that aren’t gobbled up right out of the oven. Store the muffins in a food-safe freezer bag or airtight container for up to 4 months. When you want to eat a muffin, you can thaw it overnight in the fridge or microwave it for 30 seconds straight from the freezer. If you want to use a toaster oven to heat up a muffin, I would still thaw it first and then bake at 300°F for ~5 minutes or until heated through.

A hand holding up a paleo pumpkin chocolate chip muffin.

Love Pumpkin Recipes?

I have a few more fall-inspired paleo dessert recipes to use up your leftover canned pumpkin purée:

  • Pumpkin Carrot Muffins
  • Pumpkin Muffins
  • Pumpkin, Coconut, and Maple Custard Cups

Let’s bake pumpkin chocolate chip muffins!

Serves 12

Ingredients:

  • 2½ cups (280 g) finely ground almond flour
  • 2 teaspoons pumpkin spice blend
  • 1 teaspoon baking soda
  • ½ teaspoon cream of tartar or 1 teaspoon lemon juice (added to wet ingredients)
  • ¼ teaspoon Diamond Crystal kosher salt
  • 1 cup (245 g) canned pumpkin purée
  • ½ cup (169.5 g) honey
  • 4 large eggs
  • 1 teaspoon vanilla extract
  • 1 cup (180 grams) dark chocolate chips

Equipment

  • All my favorite tools are listed here.

Method:

Heat oven to 350ºF with the rack in the middle. Line a muffin tin with parchment muffin liners or grease it well with ghee or coconut oil.

A hand is lining a muffin tin with parchment cupcake liners.

Combine the dry ingredients in a medium bowl: almond flour, pumpkin spice blend, baking soda, cream of tartar, and salt.

Measuring the dry ingredients for paleo and gluten free pumpkin chocolate chip muffins in a silver mixing bowl.

Whisk the dry ingredients until uniform and set aside.

Whisking the dry ingredients for pumpkin chocolate chip muffins with a whisk.
In a separate large bowl, add the pumpkin purée, honey, eggs, and vanilla. (If you’re using lemon juice in place of cream of tartar, add it to this bowl.)

Adding eggs and vanilla extract to the bowl of wet ingredients for paleo and gluten free pumpkin chocolate chip muffins.

Use a hand mixer or whisk to blend everything together.

A hand mixer is blending the wet ingredients for pumpkin chocolate chip muffins, a paleo and gluten free treat.

Here’s where you have to work quickly! Add the dry ingredients to the bowl of wet ingredients…

Adding the bowl of dry ingredients to the wet ingredients for the pumpkin chocolate chip muffins.

…and mix until well combined.

Overhead shot of a hand mixer combining the dry and wet ingredients for the paleo chocolate chip muffins.
Manually fold in the chocolate chips.

Folding in the chocolate chips into the pumpkin muffin batter with a yellow silicone spatula.Divide the batter evenly into each muffin liner with a large ice cream scoop.

Using a large ice cream scoop to divide the pumpkin chocolate chip muffin batter into the muffin tin.

If you’re feeling extra, dot the top with a few bonus chocolate chips so folks know what’s inside.

Adding extra chocolate chips on top of the pumpkin chocolate chip muffins before placing them in the oven.

Don’t dawdle because the baking soda has already been activated at this point and the muffins need to get in the oven!

Placing the unbaked paleo pumpkin chocolate chip muffins into the oven.
Bake the muffins in the oven at 350°F for 25 to 30 minutes, rotating the muffin tray at the halfway mark.

Rotating a tray of gluten free pumpkin chocolate chip muffins in the oven at the halfway cooking point.

The muffins are done cooking when the tops are golden brown and a toothpick inserted into the middle comes out clean.

Checking if the grain free pumpkin chocolate chip muffin are ready with a toothpick inserted into the middle of one.
Remove the muffins from the oven and transfer the muffins to a wire cooling rack to cool.

Overhead shot of paleo, gluten free, and grain free pumpkin chocolate chip muffins cooling on a wire rack on a gray counter.

Chow down and freeze the leftovers!

A side angle shot of a dozen paleo and gluten free pumpkin chocolate chip muffins cooling on a wire rack.


Looking for more recipe ideas? Head on over to my Recipe Index. You’ll also find exclusive recipes on my iPhone and iPad app, and in my cookbooks, Nom Nom Paleo: Food for Humans (Andrews McMeel Publishing 2013), Ready or Not! (Andrews McMeel Publishing 2017), and Nom Nom Paleo: Let’s Go! (Andrews McMeel Publishing 2021).


PRINTER-FRIENDLY RECIPE CARD

A hand holding up a paleo pumpkin chocolate chip muffin.
Print Recipe
4.91 from 20 votes

Pumpkin Chocolate Chip Muffins (Paleo, Gluten Free, Grain Free)

These honey-sweetened almond flour pumpkin chocolate muffins can be made ahead and kept in the freezer so you can easily heat one up when pumpkin spice blend season hits!
Prep Time15 mins
Cook Time30 mins
Cooling time1 hr
Course: Dessert
Cuisine: American
Keyword: gluten-free, grain-free, nom nom paleo, nomnompaleo, paleo, paleo dessert, pumpkin
Servings: 12
Calories: 286kcal
Author: Michelle Tam

Ingredients

  • 2½ cups finely ground almond flour
  • 2 teaspoons pumpkin spice blend
  • 1 teaspoon baking soda
  • ½ teaspoon cream of tartar or 1 teaspoon lemon juice (added to wet ingredients)
  • ¼ teaspoon Diamond Crystal kosher salt 
  • 1 cup canned pumpkin purée
  • ½ cup honey
  • 4 large eggs
  • 1 teaspoon vanilla extract
  • 1 cup dark chocolate chips
US Customary - Metric

Instructions 

  • Heat oven to 350ºF with the rack in the middle. Line a muffin tin with parchment muffin liners or grease it well with ghee or coconut oil.
  • Combine the dry ingredients in a medium bowl: almond flour, pumpkin spice blend, baking soda, cream of tartar, and salt. Whisk the dry ingredients until uniform and set aside.
  • In a separate large bowl, add the pumpkin purée, honey, eggs, and vanilla. (If you’re using lemon juice in place of cream of tartar, add it to this bowl.) Use a hand mixer or whisk to blend everything together.
  • Here’s where you have to work quickly! Add the dry ingredients to the bowl of wet ingredients and mix until well combined.
  • Manually fold in the chocolate chips.
  • Divide the batter evenly into each muffin liner with a large ice cream scoop. If you’re feeling extra, dot the top with a few bonus chocolate chips so folks know what’s inside.
  • Bake the muffins in the oven at 350°F for 25 to 30 minutes, rotating the muffin tray at the halfway mark. The muffins are done cooking when the tops are golden brown and a toothpick inserted into the middle comes out clean.
  • Remove the muffins from the oven and transfer the muffins to a wire cooling rack to cool.

Video

Notes

Freeze the leftover muffins! Store the muffins in a food-safe freezer bag or airtight container for up to 4 months. When you want to eat a muffin, you can thaw it overnight in the fridge or microwave it for 30 seconds straight from the freezer. If you want to use a toaster oven to heat up a muffin, I would still thaw it first and then bake at 300°F for ~5 minutes or until heated through.
Tried this recipe?Mention @nomnompaleo or tag #nomnompaleo!

Nutrition

Calories: 286kcal | Carbohydrates: 27g | Protein: 8g | Fat: 18g | Fiber: 4g | Sugar: 18g
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Reader Interactions

Comments

  1. Bill says

    September 15, 2020 at 5:38 am

    5 stars
    These were great!! I only had sweet potato puree so I used that and also only had 2 cups of almond flour so I subbed half cup of coconut flour and these still turned out delicious!

    Reply
  2. Janet says

    September 15, 2020 at 5:57 pm

    They look great! I’m excited that pumpkin “everything” season is back!

    Reply
    • Tracy says

      September 17, 2020 at 4:34 am

      5 stars
      Excellent! Absolutley love the carrot pumpkin miffins too!

      Reply
  3. Kim says

    September 19, 2020 at 4:58 pm

    5 stars
    Tasty and so quick and easy to throw together using a scale. Thank you!

    Reply
  4. Maggie Grace says

    September 21, 2020 at 8:34 pm

    Nice! Thanks for the recipe! I used sorghum syrup and honey because my jar of honey was almost empty and here in Houston we are sitting in a tropical storm (Beta) and I can’t get to Costco. Anyway, I love sorghum syrup more than honey so hope it’s good!

    Reply
  5. Marilyn says

    September 21, 2020 at 9:05 pm

    Just made these and ate one fresh out of the oven . Yum ! Followed the recipe except for replacing part of the cup of chocolate chips with craisins and pecans . This is a keeper and I love that it incorporates a good amount of pumpkin not just a couple tablespoons . I think they may be even better when they cool but pretty delightful warm . Thank you. !

    Reply
  6. Hunny Zacharski says

    September 23, 2020 at 6:40 pm

    Everyone in the family loved these pumpkin muffins! They went really quickly. Super easy to make and I was happy at how they lasted in a baggie on the counter. I will make again!

    Reply
  7. Tiffani Nichols says

    September 29, 2020 at 9:15 pm

    5 stars
    Super moist. My 2 year old and 40 something husband both loved them! Will be making these again.

    Reply
  8. HEATHER J SOWERS says

    October 6, 2020 at 4:35 pm

    Michelle or others, can I use fresh pumpkin instead of canned and if so should I puree it first?

    Reply
    • Michelle Tam says

      October 6, 2020 at 4:49 pm

      You will need to cook and puree fresh pumpkin before making this recipe.

      Reply
  9. Keith says

    October 14, 2020 at 2:14 pm

    Hi. This recipe looks like your regular pumpkin muffin recipe. Does this I could play with the cup of chocolate chips and instead do a blend of chips and nuts as long as I stay within a cup and not messed up the recipe? Thanks.

    Reply
    • Michelle Tam says

      October 14, 2020 at 3:59 pm

      Definitely!

      Reply
  10. Sara says

    October 17, 2020 at 9:51 pm

    5 stars
    I subbed 1/2 cup of monkfruit sweetener for the 1/2 cup of honey and the turned out great!

    Reply
  11. Veronica says

    November 12, 2020 at 6:58 pm

    These look amazing! I can’t wait to try them. I’m so happy that they’re corn free, I’ve had a lot of difficulty finding corn-free desert options, especially more seasonal ones.

    Reply
  12. Dorothy Webster says

    October 4, 2021 at 2:12 am

    5 stars
    These are nice, I found they only needed 20 minutes in my fan forced oven.
    I dont usually have success with gluten free recipes but this one turned out great.

    Reply
  13. Cindi says

    October 10, 2021 at 12:40 am

    Can you sub maple syrup for the honey?

    Reply
    • Michelle Tam says

      October 11, 2021 at 2:49 pm

      I haven’t tried it, but it should work!

      Reply

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