3 pumpkin chocolate chip muffins on a black plate

Paleo Pumpkin Muffins are a delicious pumpkin spiced muffin with a flavor and texture similar to pumpkin pie. They are full of sugar-free chocolate chips and topped with a sprinkling of pumpkin seeds.

Paleo Pumpkin Muffins on a black plate with wrapper removed

These pumpkin muffins are great for a grab and go breakfast, or for an afternoon snack. They have a strong pumpkin and spice flavor with a hint of maple. These muffins are a great treat to serve in the fall, but also delicious year-round!

Why I made Paleo Pumpkin Muffins

Fall always puts me in the mood for all things pumpkin spiced. Lucky for me, pumpkin is an approved vegetable on the Paleo and Keto diet. This pumpkin muffin is dairy-free because I felt the need to cut down on my dairy consumption. I also wanted to see if it would take me out of my weight loss stall.

3 pumpkin chocolate chip muffins on a black plate

I love a pumpkin and chocolate combination. They are an excellent match. So, I decided to add chocolate chips in the muffins. You can leave out the chocolate chips and add chopped pecans or walnuts.

Creating a Paleo, low carb, and keto-friendly muffin recipe

While I love dairy products, I feel that dairy has stalled my weight loss. Even on keto, you can eat too much of a good thing. So, I decided to try following Paleo for a while to see how it would work out.

Paleo would allow me to add a few more foods to my diet. I felt that the addition of some fruits (other than berries) in my diet would make it easier to give up my cheese. My goal with Paleo is to stay under 50 carbohydrates a day, which has not been hard to do at all. The nutritional information is still low carb and keto with total carbs just under 7g and net carbs just under 3g!

This recipe is still a low carb keto muffin recipe. It is also considered gluten-free, grain-free. I made changes to the ingredients to reflect the desired nutritional outcome to fit the Paleo diet and have it still be keto friendly.

Tips for making Pumpkin Chocolate Chip Muffins

  • Whisk together the dry ingredients really well. Coconut flour tends to have some lumps in it and you don’t want lumps of coconut flour in your muffin.
  • Pre-measure all your ingredients before combining them to make it easy to just mix and scoop. This makes clean up easier. Just put the dirty dishes right in your sink or dishwasher after using them.
  • Stir the batter just enough to combine all the ingredients. Then add the sugar-free chocolate chips to the batter. Use two bowls, a dry mix bowl, and a wet mix bowl.

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Make these low carb muffins your way

I cut out the fat and removed the dairy from this muffin recipe. I did not add cream butter. This reduced the calories quite a bit. There are a few substitutes you could make that would not change the structure of this pumpkin muffin. Below are some suggestions.

Sweeteners: If your not Keto, then you can substitute coconut sugar or maple syrup for the golden monk fruit.

Flours: If you have a nut allergy, you can substitute tapioca flour for the almond flour. Tapioca flour is a Paleo approved flour. However, keep in mind, this increases the carbs and knocks the pumpkin muffins out of the keto range.

Muffin Topping: I used pumpkin seeds because I didn’t feel the desire to put a crumb topping on my muffin. However, some people love a streusel topping.

Other low carb breakfast recipes you may want to try

I am a big fan of muffins in the morning. I love that they are portable and filling. Fresh Raspberry Muffins and Rhubarb Muffins with Crumb Topping are keto-friendly and can be made paleo with a few substitutions. Maple Bacon Pancake Muffins are also very delicious and they fit both the Keto and Paleo diet!

Another favorite breakfast recipe that is pumpkin spiced is this Keto Pumpkin Dutch Baby. Use the coconut oil instead of butter and it is also a Paleo recipe! Or, try this Keto Dutch Baby with Chocolate and Macadamias!

Paleo Pumpkin Muffins with Chocolate Chips

If you made this recipe for Paleo Pumpkin Muffins with Chocolate Chips, please leave a star rating!

3 pumpkin chocolate chip muffins on a black plate

Paleo Pumpkin Muffins

Shelby Law Ruttan
Paleo Pumpkin Muffins are a simple and delicious breakfast recipe. They resemble pumpkin pie in flavor and are full of sugar-free chocolate chips
0 from 0 votes
Prep Time 10 mins
Cook Time 20 mins
Total Time 30 mins
Course Family Recipes
Cuisine American
Servings 12



  • Preheat to 350 degrees. Line a 12-cup muffin tin with muffin liners.
  • In a medium bowl, mix together eggs, pumpkin puree, and maple extract.
  • In a large bowl, add almond flour, coconut flour, monkfruit, pumpkin pie spice, salt, and baking powder. Whisk to combine and break up any lumps.
  • Add wet ingredients to the flour mixture and stir to combine. Fold in sugar-free chocolate ships.
  • With a 1/4 cup size scoop, add the pumpkin muffin batter to the paper-lined muffin pan.
  • Bake for 20 minutes or until a toothpick inserted into the center of the muffin comes out clean.
  • Cool on a cooling rack and store in an airtight container.


2.96 Net Carbs per serving
Keyword Paleo Pumpkin Muffins
Tried this recipe?Let us know how it was!

About the Author: Shelby Law Ruttan

Honeybunch Hunts is a website dedicated to Hunting, Homesteading and Harvesting. Written by Shelby Law Ruttan, author and owner of Grumpy’s Honeybunch, she (Honeybunch) and Phil (Grumpy) have come together in a joint effort to share their knowledge and experience from the woods, to the garden, to the table.


  1. Anonymous October 6, 2019 at 8:40 pm - Reply


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  8. Lena October 30, 2020 at 3:19 pm - Reply

    Every time I print one of your recipes the ingredient list and the headline name of recipe print is so light, that I can barely read it. No I am not running out of toner. I think you have your recipe formatted to be shaded when it is printed, the headings “Ingredients” and “Instructions” are bold and are fine; heading and the text that is so light in print. Could you look into this. Maybe I am only person who has noticed this?

    • Shelby Law Ruttan October 30, 2020 at 5:51 pm - Reply

      Hi Lena, yes, I will look into this. It may be the setting on the recipe card and I will likely have to have my tech look at it. Thanks for letting me know.

  9. […] Paleo Pumpkin Muffins […]

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Shelby I'm Shelby, author of Honeybunch Hunts. I love hunting, homesteading, and harvesting and am sharing my experiences and recipes with you! I hope you will join my journey and find something you will love! Honeybunch Hunts is a website dedicated to Hunting, Homesteading and... read more

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