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Low Carb Pumpkin Chocolate Chip Muffins

These delicious Keto chocolate chip pumpkin muffins are a great way to start off your morning. Easy to make, healthy, and tasty, they made a great snack. 

Keto Pumpkin Chocolate Chip Muffins

I’m going to tell you the truth about these pumpkin chocolate chip muffins, they actually started off as pumpkin chocolate chip bread. But after making it 4 different times, it just wasn’t working right. The flavor was perfect but it just wasn’t rising the way I wanted it to. At this point, I was so frustrated that I decided let’s turn this bread into some muffins instead. 

So for the 5th time, I whipped up another batch and poured them into a sprayed muffin tin. And 20 minutes later I had perfectly yummy pumpkin muffins! Finally, I got it done right!

Don’t worry though I’m not going to give up on my pumpkin bread, and hopefully I will have perfected that soon for all of you pumpkin lovers. 

These muffins are a great option for a quick, on-the-go breakfast or if you are looking for a sweet treat later in the day.

How Many Carbs are in Pumpkin Muffins with Chocolate Chips?

They taste so good that you might automatically think they are full of calories and higher in carbs. But it’s the exact opposite, for 1 pumpkin chocolate chip muffin, it’s only 3.3 NET CARBS and 133 calories. Not bad at all right? 

Even if you’re not counting carbs or eating light, these healthy pumpkin muffins are a great lighter option instead of other heavier fall desserts/breakfast options. 

What Ingredients are in Low Carb Pumpkin Chocolate Chip Muffins?

Pumpkin Chocolate Chip Muffins on a rack
  • Almond Flour  
  • Coconut Oil 
  • Eggs 
  • Pumpkin 
  • Salt 
  • Baking Soda 
  • Baking Powder  
  • Nutmeg
  • Pumpkin Pie Spice
  • Xanthan Gum
  • Lily’s Dark Chocolate Chips 

Is it Better to Use Almond Flour or Coconut Flour for Keto Pumpkin Muffins?

If you’ve been reading some of my other articles you will know that my go-to low carb flour is always almond flour. I’ve found that almond flour is the most like regular flour in these muffins. Typically it’s about a 1-1 substitution, but sometimes you need to make some adjustments. 

Now you can use coconut flour, but it’s something that I haven’t mastered yet. What I do know though is that coconut flour isn’t a 1-1 substitution. You use a lot less and you need to let it sit and absorb some of the liquid before baking. 

It is possible to use a combo of almond flour and coconut flour. Remember though you will need more almond flour and less coconut flour. It’s not an exact science and it can change depending on the recipe, but a good rule of thumb is about ¼ cup of coconut flour to about 1 cup of almond flour. 

Which is the Best Fat for these Muffins?

how to make Pumpkin Chocolate Chip Muffins

When making these healthy pumpkin muffins you can make them with coconut oil, butter or ghee. I chose to use coconut oil because I wanted them to be dairy-free, but if that’s not an issue for you then you can use butter. 

Best Chocolate Chips for Keto Muffins?

My favorite go-to chocolate chips for these pumpkin muffins are Lily’s Dark Chocolate Chips. They are sugar-free, but sweetened with stevia. And surprisingly they don’t really have an aftertaste at all.

For 60 chips (which is a lot) they are only 5 net carbs. 

How to Make Keto Pumpkin Chocolate Chip Muffins

ingredients for Pumpkin Chocolate Chip Muffins

This is a pretty simple recipe and only takes about 10 minutes to prep. 

Start off by preheating the oven to 325. Don’t go any higher than this, otherwise, they will burn on the top before cooking fully in the middle. 

Now measure out the coconut oil and melt it down to fill ¼ cup. Microwave it for a few seconds at a time until it’s all liquid.

In a medium bowl combine coconut oil and sweetener. Stir it up well.

Add eggs and pumpkin to oil mixture and stir it all together. 

Now in a separate bowl, combine almond flour, salt, baking soda, baking powder, xanthan gum, pumpkin pie spice. Stir all the dry ingredients well.

Once well combined, add the dry ingredients to the pumpkin mixture. Mix the batter up until all ingredients are combined. 

Gently fold in the chocolate chips.

Spray a muffin pan with baking spray. Then using a cookie scoop, start scooping the muffin batter into the pan. You should end up with about 15 muffins. 

Bake on 325 degrees for about 20-25 minutes depending on your oven. Just keep an eye on them. Once they look done, then let them sit on top of the stove to cool. Once cooled you can take them out of the muffin pan. 

Variations on Pumpkin Chocolate Chip Muffins

You may not want chocolate chips in your muffins, and that’s ok, so just omit them if you prefer. Or if you like nuts then add in some walnuts or pecans. That’s how my mom prefers them, her philosophy is the more nuts, the butter. 

If you aren’t counting carbs and sugar then another nice addition you can make is some dried fruit, like craisins. 

Other Diets this Recipe is Good for

sugar free Pumpkin Chocolate Chip Muffins

Not only are these pumpkin chocolate chip muffins are perfect keto snack, but they are also many other things as well. 

I use a low carb sweetener, and chocolate chips that are sugar-free but sweetened with stevia, so it makes these muffins sugar-free. 

Using almond flour makes these tasty muffins great for those who are gluten-free. And because I use coconut oil instead of butter they are also dairy-free

How to Store Keto Pumpkin Muffins

These keto pumpkin muffins are easy to store. Put them into a Ziploc bag and keep them on your counter or in your fridge. They will last up to about a week, especially if kept in the fridge. 

Can I Freeze Pumpkin Chocolate Chip Muffins?

Yes, absolutely you can freeze them! Actually, I highly recommend you freezing them if you have any leftovers. You can freeze them in a Ziploc bag, and when ready to eat a frozen muffin just place them on the counter to thaw or pop them in the microwave for a few seconds. 

With my last batch, I froze about a half dozen of them and my dad kept taking one out every night after dinner before I knew it they were all gone. 

My favorite though is to have them in the morning with my coffee, it’s the perfect combo especially on those cold mornings. 

best Keto Pumpkin Chocolate Chip Muffins

Other Low Carb Pumpkin Recipes:

If you’re in the mood for some other Keto-friendly Pumpkin Recipes, check out our:

All of them are Keto-friendly and low carb, and will have your friends raving!

Low Carb Muffin Recipes

If you’re in the mood for some other Keto-friendly muffins, check out our:

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Keto Pumpkin Chocolate Chip Muffins recipe

Low Carb Pumpkin Chocolate Chip Muffins

  • Author: Stephanie Parlegreco
  • Prep Time: 10 minutes
  • Cook Time: 20-25 minutes
  • Total Time: 30-35 minutes
  • Yield: 15 Muffins (1 Muffin per Serving) 1x
Save Recipe


Delicious keto pumpkin chocolate chip muffins are a great way to start off your morning. Easy to make, healthy, and tasty, they made a great snack.


  • 1 ½ cups almond flour
  • ¼ cup coconut oil, melted
  • 1 ½ cups monk fruit sweetener 
  • 1 cup pumpkin purée
  • 2 large eggs
  • 1 tsp salt
  • ½ tsp baking soda
  • 1 tsp baking powder
  • ¼ tsp xanthan gum 
  • 2 tsp pumpkin pie spice
  • cup Lily’s Dark Chocolate Chips




You can add in nuts, or leave the chocolate chips out completely

A combination of almond flour and coconut flour can be used

I use coconut oil, but you can substitute it with butter or ghee 

Don’t bake the muffins at a temperature any higher than 325 degrees otherwise, they will burn

  • Category: Breakfast
  • Method: Baking
  • Cuisine: American

Keywords: Pumpkin Chocolate Chip Muffins, Keto Pumpkin Chocolate Chip Muffins, Low Carb Pumpkin Chocolate Chip Muffins, Low Carb Chocolate Chip Pumpkin Muffins, Chocolate Chip Pumpkin Muffins recipe, Keto Chocolate Chip Pumpkin Muffins, Pumpkin Chocolate Chip Muffins recipe, best Pumpkin Chocolate Chip Muffins recipe, easy Pumpkin Chocolate Chip Muffins

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Recipe rating

Robin Newman

Sunday 18th of October 2020

Tasty, but too sweet for my family. Next time I will make it with 1/3 of the sweetener.

Leigh Oskwarek

Sunday 18th of October 2020

Hi Robin, Thanks for trying our recipe for low carb pumpkin chocolate chip muffins and thanks for your input. Sometimes I think a recipe is too sweet because I have been off of sugar for 3 years, so then I just use less sweetener.

Deborah Castle

Monday 5th of October 2020

Ingredient list doesn’t state amount of chocolate chips.

Leigh Oskwarek

Tuesday 6th of October 2020

Hi Deborah, We apologize for not listing the number of chocolate chips in our pumpkin chocolate chip muffins. There are 2/3 of a cup in the entire recipe. Thank you for taking the time to try our recipe. We welcome you back to our site anytime.