Keto Pumpkin Chocolate Chip Muffins

These keto pumpkin chocolate chip muffins are soft, tender, warmly spiced, and filled with rich sugar-free chocolate chips. They give you all the flavor of classic pumpkin muffins without the sugar, gluten, or high carbs.

Made with almond flour, golden flax meal, pumpkin puree, and a sugar substitute, these low-carb pumpkin muffins have a lovely texture and just the right amount of fall flavor.

They are perfect for breakfast, an afternoon snack, lunchboxes, or even a simple keto dessert with a hot cup of coffee or tea.

I have an entire collection of keto muffin recipes you may want to check out.

Why You'll Love These Keto Pumpkin Chocolate Chip Muffins

If you love pumpkin season but want to keep your carbs low, this recipe is a great one to add to your fall baking list.

These muffins are:

• Keto-friendly
• Low in carbs
• Gluten-free
• Sugar-free
• Made with real pumpkin puree
• Packed with warm pumpkin spice flavor
• Studded with sugar-free chocolate chips
• Freezer-friendly

The combination of pumpkin, cinnamon, ginger, nutmeg, cloves, and chocolate makes these muffins feel like a special treat while still fitting beautifully into a keto lifestyle.

And at only 2.1 net carbs per muffin, they are a delicious way to enjoy pumpkin without the sugar crash.

Keto Pumpkin Muffins With Chocolate Chips

Pumpkin and chocolate are such a delicious match. The pumpkin puree keeps the muffins moist, while the sugar-free chocolate chips add just enough richness to make them feel extra special.

Since pumpkin is naturally higher in carbs than some other keto-friendly ingredients, this recipe uses just the right amount to give you that classic pumpkin flavor while keeping the carb count low.

The almond flour and golden flax meal work together to create a soft but sturdy muffin crumb. The flax meal also helps absorb some of the moisture from the pumpkin, which is important when baking keto muffins.

Ingredients Needed

Disclosure: Some of the links below are affiliate links, meaning, at no additional cost to you, I will earn a commission if you click through and make a purchase. 

• Canned Pumpkin Puree
• Granulated Sugar Substitute
• Unsalted Melted Butter
• Vanilla Extract
• Eggs, Room Temperature
• Finely Milled Almond Flour
• Golden Flax Meal: Golden flax meal is important for this recipe because it helps add fiber and structure while keeping the muffins tender. I do not recommend using regular flax meal because it can give the muffins a gummy texture.
• Baking Powder
• Cinnamon Powder
• Ground Ginger
• Ground Nutmeg
• Ground Cloves
• Sea Salt
• Sugar-Free Chocolate Chips

Use Pumpkin Puree, Not Pumpkin Pie Filling

Be sure to use 100% canned pumpkin puree for this recipe and not pumpkin pie filling.

Pumpkin pie filling contains added sugar and spices, which makes it much higher in carbs and not suitable for keto baking.

Plain pumpkin puree gives these muffins the right texture, flavor, and moisture without adding unnecessary sugar.

Sweetener Options

For thes keto pumpkin chocolate chip muffins, I recommend using a granulated sugar substitute that measures cup-for-cup like regular sugar.

A monk fruit and erythritol blend or allulose blend work well.

If you prefer a stevia based sweetener, I recommend you reduce the amount by half since it is doubly sweet.

Check out our keto sweetener guide for a more detailed explanation.

Sugar-Free Chocolate Chip Options

For these keto pumpkin chocolate chip muffins, I recommend using sugar-free chocolate chips that melt well and have a rich chocolate flavor. Lily's semi-sweet chocolate chips are a great option because they add just the right amount of sweetness without overpowering the pumpkin spice flavor.

If you prefer a deeper chocolate taste, these dark chocolate chips also work beautifully in this recipe. They pair especially well with the cinnamon, ginger, nutmeg, and cloves.

Hershey's sugar-free chocolate chips are another option if that is what you have on hand. Just be sure to choose a sugar-free chocolate chip that fits your personal keto goals.

Mini sugar-free chocolate chips are my favorite choice for these muffins because they distribute more evenly throughout the batter and give you a little chocolate in every bite.

Why The Batter Is Thick

This keto pumpkin chocolate chip muffin batter will be thick, and that is completely normal.

Almond flour and golden flax meal absorb moisture differently than traditional wheat flour. The pumpkin puree also adds moisture, so the batter may look dense before baking.

Do not add extra liquid. Once baked, the muffins will have a tender texture and hold together well after cooling.

How To Make Keto Pumpkin Chocolate Chip Muffins

To make these muffins, start by preheating the oven to 400 degrees and lining two muffin tins with 18 muffin liners.

In a large mixing bowl, beat the pumpkin puree, granulated sugar substitute, melted butter, and vanilla extract until everything is well combined.

Next, add the eggs one at a time, beating well after each addition. This helps create a smoother batter and gives the muffins a better texture.

Add the almond flour, golden flax meal, baking powder, cinnamon, ginger, nutmeg, cloves, and sea salt to the wet ingredients. Mix until the batter is fully combined. The batter will be thick, so be sure to scrape the sides of the bowl as needed.

Fold in the sugar-free chocolate chips, making sure they are evenly distributed throughout the batter.

Divide the batter evenly among the prepared muffin cups, filling each about ¾ full.

Bake the muffins at 400 degrees for the first 5 minutes. Then, without removing the muffins from the oven, reduce the temperature to 350 degrees and continue baking until the muffins are golden and an inserted toothpick comes out clean.

Allow the muffins to cool in the pan for about 10 minutes before transferring them to a baking rack to cool completely.

How To Get Rounded Muffin Tops

Starting the muffins at a higher oven temperature helps give them a nice lift. Baking them at 400 degrees for the first few minutes allows the batter to rise quickly.

After the first 5 minutes, lowering the oven temperature to 350 degrees allows the muffins to finish baking evenly without becoming too brown.

Since keto muffins do not rise the same way traditional wheat-based muffins do, this method helps create a fuller muffin top.

Tips For The Best Gluten-Free Pumpkin Muffins

For the best results, use 100% canned pumpkin puree, not pumpkin pie filling. Pumpkin pie filling contains added sugar and other ingredients that are not keto-friendly and will change the carb count and flavor of these muffins.

You'll also want to use finely milled almond flour rather than almond meal. A finer almond flour gives these keto pumpkin chocolate chip muffins a softer crumb and a better overall texture.

Once the dry ingredients are added, mix the batter just until everything is fully combined. Overmixing can make keto muffins more dense.

Keep in mind that this batter will be thick because of the almond flour, golden flax meal, and pumpkin puree. This is normal, so do not be tempted to add extra liquid.

How To Store Low-Carb Pumpkin Chocolate Chip Muffins

Store any leftover muffins in an airtight container in the refrigerator for up to 5 days.

Because these muffins are made with pumpkin puree and low-carb flours, they stay freshest when refrigerated.

You can enjoy them cold, at room temperature, or gently warmed before serving.

Can You Freeze These Pumpkin Chocolate Chip Keto Muffins?

Yes, these muffins freeze well for up to 3 weeks.

For best results, wrap the muffins individually and place them in a freezer-safe container or bag. This makes it easy to grab one muffin at a time when you need a quick keto breakfast or snack.

Thaw the muffins overnight in the refrigerator or on the counter before serving.

More Keto Pumpkin Recipes To Try

Be sure to check out our entire collection of keto pumpkin recipes. Pumpkin is one of those flavors that makes sugar-free baking feel extra special, especially during the fall season.

If you enjoy these keto pumpkin chocolate chip muffins, you may also want to try more low-carb pumpkin recipes like:

• Keto Pumpkin Chocolate Chip Cookies
• Keto Pumpkin Muffins
• Keto Pumpkin Spice Donuts
• Keto Pumpkin Cheesecake Pie
• Keto Coconut Flour Pumpkin Bread

Tag Us

I sure hope you'll give this recipe a try. When you do, be sure to tag us on Instagram and Facebook. It truly encourages me to keep sharing and perfecting these keto recipes for you.

You can also visit our Amazon Store for some of our favorite keto baking tools, pantry staples, and low-carb recommendations.

Grab Our Books & Recipe App

In case you don't know, we've authored two keto cookbooks, Essential Keto Bread and Essential Keto Desserts, both inspired by your requests over the years.

You can also find even more easy keto recipes for breakfast, lunch, dinner, snacks, and desserts inside the  Fit to Serve Group App on  iOS and Android.

Join Our Jesus And Keto Movement

Looking for support on your keto journey? We invite you to join our private Jesus and Keto Facebook group, where we encourage one another to pursue lasting transformation through faith, grace, and a low-carb lifestyle.

Be sure to also request our FREE Jesus and Keto E-Book: First 7 Days. We pray it blesses you.