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!

A hand holding up a paleo pumpkin chocolate chip muffin.

Ingredients

  • Finely ground almond flour
  • Canned pumpkin purée: I like Libby’s brand the best
  • Pumpkin spice blend
  • Honey
  • Eggs
  • Vanilla extract
  • Dark chocolate chips
  • Baking soda
  • Cream of tartar or 1 teaspoon lemon juice (added to wet ingredients)
  • Diamond Crystal kosher salt

How to make pumpkin chocolate chip muffins

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!

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

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.


Looking for more recipe ideas? Head on over to my Recipe Index. You’ll also find exclusive recipes 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 2022).


PRINTER-FRIENDLY RECIPE CARD

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

4.82 from 27 votes
Prep Time15 minutes
Cook Time30 minutes
Cooling time1 hour
Servings 12
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!

Ingredients 
 

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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.

Nutrition

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

Nutrition information is automatically calculated, so should only be used as an approximation.

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About Michelle Tam

Hello! My name is Michelle Tam, and I love to eat. I think about food all the time. It borders on obsession. I’ve always loved the sights and smells of the kitchen. My mother was (and is) an excellent cook, and as a kid, I was her little shadow as she prepared supper each night. From her, I gained a deep, abiding love for magically transforming pantry items into mouth-watering family meals.

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20 Comments

  1. 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.

  2. 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.

    1. It would change up the texture slightly since the honey adds liquid to the recipe. Maple syrup would be a better sub than coconut sugar.