Pumpkin Chocolate Chip Muffins (Keto + Gluten Free)

This content originally appeared on Low Carb Yum. Republished with permission.

Bake these pumpkin chocolate chip muffins for an indulgent, seasonal recipe. Made with low-carb chocolate chips, pumpkin puree, and just a hint of vanilla, this autumn-inspired recipe is sure to be a new favorite.

Why You’ll Love These Pumpkin Chocolate Chip Muffins

Pumpkin and chocolate is a match made in heaven!

And you can harness this delicious combination with my chocolate chip pumpkin muffins recipe.

This simple baked good is incredibly easy to make, using canned pumpkin for a perfectly moist consistency. Plus, it’s naturally gluten-free, keeping things low-carb and celiac-friendly.

Best of all, these mouth-watering muffins contain just 3 grams of net carbs per muffin. In other words, you can eat them guilt-free for a sweet snack, satisfying dessert, or grab-and-go breakfast option.

In this post, I’m sharing how to make these decadent pumpkin chocolate chip muffins, complete with yummy serving suggestions, fun variations, and baking tips for the perfect muffins – every time!

Plus, dig into some of my very favorite muffin recipes to inspire an entire season’s worth of baking.

Note: For more pumpkin recipes and information on eating pumpkin on a low-carb diet, check out my post on Is Pumpkin Keto-Friendly?

Ingredients In Pumpkin Chocolate Chip Muffins

These muffins are made with 100% keto-friendly ingredients (score!). Here’s everything you’ll need to gather:

Almond flour

The base of this recipe is almond flour. I love using this naturally gluten-free flour because it’s low-carb, easy to source, and provides a satisfying, chewy texture to baked goods.

You can use almond flour as an easy substitution for wheat flour in your favorite recipes to make them keto.

Sugar-free sweetener

For a sweetener, I use a low-carb sugar substitute like erythritol or monk fruit. These ingredients add a great sweetness in a keto-friendly formula.

Both brown sugar and white sugar low-carb sweeteners would work well in this recipe.

Leavening agents

To leaven your muffins, this recipe calls for both baking powder and baking soda. Despite their floury appearances, both ingredients are totally keto-approved.

Flavor enhancers

I use a bit of sea salt to enhance all of the flavors in these pumpkin muffins.

Vanilla extract adds even more yummy flavor.

Pumpkin puree

Canned pumpkin puree is an excellent keto baking ingredient because it’s low-carb and adds amazing moisture to your recipe.

Coconut oil

For added moisture and healthy fat content, a bit of coconut oil can make all of the difference!


This recipe calls for eggs as a binding ingredient. This binder is especially important in gluten-free baking as it will keep your muffins from crumbling as they cool.

Eggs also add a bit of welcome protein content to your recipe.

Sugar-free chocolate chips

Sugar-free chocolate chips are the perfect finishing touch to your muffin batter! You can use any keto-friendly variety you prefer, from semi-sweet chocolate chips to milk chocolate chips.

No matter the type, I always prefer mini chocolate chips. I find they provide the perfect bite in your finished muffins!

Baking Tips

Before you get baking, here are a few quick tips to help yield the best results possible:

Make sure that your coconut oil has both melted and slightly cooled before adding it to the rest of your wet ingredients. This will ensure an even mix without any clumps.
Resist the urge to over-mix your batter. Stop mixing when your ingredients are combined to keep the texture moist and fluffy.
Store these muffins in an airtight container to keep them moist and fresh. They will keep for 3-4 days on the counter or even longer when refrigerated!

How To Make Pumpkin Chocolate Chip Muffins

Ready to get baking? Here are the easy steps to creating these delicious pumpkin muffins:

Prep your baking pan

Begin by preheating your oven to 350°F and lining your muffin tin with paper liners. If you don’t have paper liners, you could simply grease your tin with a bit of oil or butter.

Mix dry ingredients

Next, prepare your dry ingredients in a large mixing bowl.

In your bowl, add almond flour, baking powder, baking soda, sugar-free sweetener, and salt.

Mix until well combined, making sure to whisk away any lumps.

Whisk wet ingredients

Then, grab a medium bowl for your wet ingredients. Add pumpkin puree, eggs, vanilla extract, and melted coconut oil.

Whisk until completely incorporated. Then, use a spatula to add this wet mixture to your dry mixture. Mix until you form a smooth batter.

Fold in chocolate chips

Finally, fold your sugar-free chocolate chips into your muffin batter. Make sure your chips are evenly distributed!

Fill and bake

Now it’s time to bake!

Pour your prepared muffin batter into your lined muffin tray, filling each cup about three-quarters full.

Then, it’s as easy as popping them into your pre-heated oven.

You’ll know your muffins are fully baked when you insert a toothpick into the center of a muffin, and it comes out clean.

Remove from oven and cool

Remove your muffins from the oven, setting them on a heat-safe surface to cool for a few minutes in the pan.

After this, remove your muffins from their tray and place them on a wire rack to finish cooling; this will keep them from overcooking.

Once they’ve cooled completely, you’re ready to chow down!

How To Serve Pumpkin Chocolate Chip Muffins

Ready to enjoy some scrumptious muffins? Enjoy a pumpkin chocolate chip muffin with a tasty seasonal drink like my keto pumpkin spice lattelow carb Starbucks salted caramel mocha, or spiced gingerbread coffee.

These pumpkin muffins would also be a delicious addition to a holiday dessert spread, with sweet pairings including low carb pecan piezucchini keto apple crisp, and gluten free pumpkin cookies.

Lastly, these muffins have great macros that make them suitable for everyday breakfast! Eat one with your favorite morning drink like bulletproof keto coffeechai masala tea, or iced keto matcha green tea latte.

Pumpkin Chocolate Chip Muffin Variations

Feel free to get creative with this pumpkin muffin recipe! Here are a few fun variations that you can try:

Adjust measurements of sugar-free sweeteners depending on how sweet you like your muffins.
Swap chocolate chips for walnut pieces for a different flavor combination.
Indulge in your pumpkin spice fantasies by adding pumpkin pie spice to your batter.
Include keto white chocolate chips for a yummy addition!
For mini muffins, reduce your baking time to about 11 minutes.


These are the questions I get the most about my delicious low-carb pumpkin chocolate chip muffins. Don’t see your question answered here? Feel free to leave yours in the comments down below.

What are the best keto chocolate chip brands?

One of the best things about the keto diet going mainstream is the sheer amount of keto-friendly alternatives now available.

Some of my favorite low-carb chocolate chips include Choc Zero Keto Baking ChipsLily’s Chips, and Hu’s Chocolate Chips.

These brands contain wide varieties of sugar-free keto chocolate chips, including white chocolate, milk, chocolate, and semi-sweet chocolate.

Is pumpkin keto-friendly?

Good news….pumpkin is a keto-friendly ingredient! You can use it in baked goods, low-carb pasta, and creamy soup recipes. Pumpkin contains just 6 grams of net carbs per serving, making it an easy ingredient to incorporate into your meal plan.

Just be sure to always check ingredients and macronutrients when buying canned pumpkin puree. Some varieties may include added sugars for baking purposes that you’ll want to steer clear of!

Can you eat muffins on a keto diet?

While traditional muffins are not keto-friendly, there are tons of delicious low-carb muffin recipes for you to enjoy!

These are just some of my favorite keto muffin recipes:

– Gluten-Free Zucchini Blueberry Muffins
– Peanut Butter Keto Chocolate Chip Muffins
– Keto Breakfast Muffins with Cottage Cheese
– Keto Carrot Cake Muffins with Cream Cheese Filling
– Healthy Banana Muffins

How do you prevent pumpkin chocolate chip muffins from sticking to the pan?

A foolproof way to prevent sticking is to use paper muffin liners in your pan. Muffins will slip easily out of the pan without any breakage!

Another alternative is to use cooking oil or butter to grease the pan, though it doesn’t guarantee the same results.

Love This Pumpkin Chocolate Chip Muffins Recipe? Try These!

If you’re inspired by this recipe, I have a ton of low-carb muffin recipes ready for you to devour. Start with some of these tasty offerings:

Keto Blueberry Cream Cheese Muffins taste like delicious mini cheesecakes stuffed with juicy blueberries for a heavenly combination.
Strawberry Jam Muffins are filled with sugar-free strawberry jam for a burst of fruity flavor with each bite. Grab one as a snack or easy breakfast.
Keto Chocolate Muffins Recipe is filled with healthy fats like avocado and cream for a macro-friendly recipe. It’s a delicious way to enjoy chocolate on a keto diet.
Almond Flour Muffins make a delicious side to a low-carb dinner, especially when paired with a knob of butter.
Cranberry Pumpkin Muffins With Coconut Flour are perfectly autumnal, with a warm spice blend and low-carb sweetener.


Pumpkin Chocolate Chip Muffins (Keto + Gluten Free)

Bake these pumpkin chocolate chip muffins for an indulgent, seasonal recipe. Made with low-carb chocolate chips, pumpkin puree, and just a hint of vanilla, this autumn-inspired recipe is sure to be a new favorite.
Course Breakfast, Snack
Cuisine American
Keyword Gluten-Free
Prep Time 10 minutes minutes
Cook Time 18 minutes minutes
Servings 10 muffins
Calories 216kcal


2 cups almond flour cup sugar-free sweetener such as erythritol or monk fruit1 teaspoon baking powder½ teaspoon baking soda¼ teaspoon salt½ cup pure pumpkin puree¼ cup coconut oil melted3 large eggs1 teaspoon vanilla extract½ cup sugar-free chocolate chips


Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners.
In a mixing bowl, combine the almond flour, sugar-free sweetener, baking powder, baking soda, and salt. Mix well to remove any lumps.
In a separate bowl, whisk together the pure pumpkin puree, melted coconut oil, eggs, and vanilla extract until well combined.
Add the wet ingredients to the dry ingredients and mix until a smooth batter forms.
Fold in the sugar-free chocolate chips until evenly distributed throughout the batter.
Divide the batter equally among the muffin cups, filling each about three-quarters full.
Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Remove the muffins from the oven and allow them to cool in the pan for a few minutes. Then transfer them to a wire rack to cool completely.


Ensure that your coconut oil is melted and cooled slightly before adding it to the wet ingredients.
Feel free to adjust the amount of sugar-free sweetener according to your desired level of sweetness.
If you prefer, you can substitute the sugar-free chocolate chips with nuts or other toppings of your choice.
Store the cooled muffins in an airtight container at room temperature for up to 3-4 days, or refrigerate for a longer shelf life.


Low Carb Sweeteners | Keto Sweetener Conversion Chart

Additional Info

Net Carbs: 2 g
% Carbs: 3.9 %
% Protein: 13.5 %
% Fat: 82.6 %
SmartPoints: 8


Nutritional information for the recipe is provided as a courtesy and is approximate only. We cannot guarantee the accuracy of the nutritional information given for any recipe on this site. Erythritol carbs are not included in carb counts as it has been shown not to impact blood sugar. Net carbs are the total carbs minus fiber.


Serving: 10g | Sodium: 176mg | Calcium: 88mg | Vitamin C: 1mg | Vitamin A: 1978IU | Sugar: 1g | Fiber: 4g | Potassium: 99mg | Cholesterol: 49mg | Calories: 216kcal | Trans Fat: 0.01g | Monounsaturated Fat: 2g | Polyunsaturated Fat: 0.5g | Saturated Fat: 9g | Fat: 19g | Protein: 7g | Carbohydrates: 6g | Iron: 2mg

Please note that the nutritional information may vary depending
on the specific brands of products used. We encourage everyone to check specific
product labels in calculating the exact nutritional information.

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