The Best Keto Pumpkin Muffins

Keto pumpkin muffins on a tray.

Master the perfect almond flour pumpkin muffins recipe that will make even the least basic pumpkin lover, swoon. They’re the best light, airy, sugar free and grain free style keto pumpkin bread you will want to make over and over again.

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I don’t care what your “basic” status is come fall (or anytime), but I do care if you make this keto pumpkin bread recipe or not.

Why? Because you are 100% doing yourself a disservice by not making these muffins a part of your life.

Now, there are a handful of other incredible pumpkin recipes here at Bon Appeteach. While I LOVE these pumpkin bread (cookie) bars or these Keto pumpkin bread scones, the world needed to have more low carb pumpkin bread baked goods in it. Thus this epic muffin.

Keto pumpkin muffin cut in half on a tray.

The muffins are light, fluffy, and somewhat cake like. They are moist from the pumpkin puree but not heavy. I especially love the delicious keto candied pecan topping (optional… but highly, HIGHLY recommended) to tie it all together and pair with a keto pumpkin spice syrup based latte on a cool morning!

Seriously, how amazing does this sound? Grab all the detailed tips and techniques for making these muffins below. Read through to understand more keto baking tricks and find the complete recipe at the bottom of the page.

“School” Supplies:

  • Muffin Tin
  • Muffin Liners
  • Large Mixing Bowl
  • Stand Mixer or Hand Mixer
  • Measuring Cups/ Spoons

“Class” Notes:

Let’s dive into basic keto staple ingredients, discuss substitutions, and outline how to assemble the best keto pumpkin muffins you’re ever going to eat!


Pumpkin Puree- This is pretty standard and you can’t really go wrong with which brand you buy. Net carbs may vary slightly from different brands but are all fairly similar when only using 1/2 cup. Just make sure you use a puree and not pumpkin pie filling.

Pumpkin Pie Spice- You can easily make your own spice blend with cinnamon, nutmeg, ginger, and allspice. But I also keep a blend on hand. Use what works and make sure to spice up the muffins to pump up the pumpkin flavor.

Cream Cheese- I do use cream cheese in this recipe to help with structure, binding, and moisture because they are gluten free. If you’re looking for a dairy free alternative, try a coconut milk yogurt as a substitution. While the batter may need slightly more baking time, this should still work fairly well in comparison.

Butter- Make sure your butter is softened, but not melted. You can do this quickly by microwaving on half power for about 20-30 seconds. The softened butter is better for creaming and helping to dissolve the low carb sweetener. If it’s too cold it gets chunky and too hot, it changes the texture of the dough.

Vanilla- This is used strictly as a flavor enhancer. Just like when you add vanilla to something chocolate based, adding vanilla to this pumpkin muffin helps amplify the pumpkin flavor.

Keto Pumpkin Muffin ingredients.

Eggs- While I should say you need to use room temperature eggs, I often forget myself. What I will suggest is to beat each egg into your mixture one at a time. This helps incorporate air and keeps the batter light and fluffy. If you can have room temp eggs, well even better!

Almond Flour – These are gluten free and keto friendly using almond flour as the base. Almond flour is my go to and works the best. Coconut flour will not be a good substitute here as it absorbs liquid differently.

Low Carb Sweeteners- My go to is usually erythritol/monk fruit combo. This is my personal favorite for general baked goods and typically use Lakanto brand. I do however prefer allulose for the “candied” pecan topping. It caramelizes like regular sugar and doesn’t recrystallize the way the other brands do.

Not into low carb sweeteners, but want this to be a friendly paleo pumpkin muffin? Sub with maple syrup or try coconut sugar instead as an option to fit your lifestyle.

Baking Powder- Used as a leavening agent, standard in most bake goods.

Salt– Everything always needs a little salt to balance out the flavor!

Making the Muffins-

I use a stand mixer with the whisk attachment to make these muffins. It makes a large amount of batter and easily comes together within 10 to 15 minutes. You can easily use a hand mixer and a larger mixing bowl instead.

Start by creaming together the butter, low carb sweetener (lakanto is my suggestion), pumpkin puree, and the softened cream cheese. Mix well until combined and not lumpy. Add in your pumpkin spices and vanilla.

Keto Pumpkin Muffin wet ingredients in a mixer.

After the liquid ingredients are mixed together, add in your five eggs, one at a time and let it mix well in between each addition. Brush down the sides as you need to with a rubber spatula to make sure everything is equally incorporated.

Finish it off with your dry ingredients of almond flour, salt, and baking powder. The mixture will be thicker than a standard cake batter but should be smooth all the way through.

Keto Pumpkin Muffin batter ingredients.

Preheat your oven to 350 F. and decide to use larger or standard muffin tins. Muffin liners are definitely a must, otherwise these can stick to the pan so keep that in mind.

Use a large 1/4 cup to help you fill larger muffin tins. Your goal is to fill these and leave about 1/2 inch from the top or so, unlike standard muffins. While these rise, they won’t rise as much as a baked good with gluten.

Keto pumpkin muffin batter in the muffin tin.

For the topping, I chose to mix in chopped pecans and pepitas/ shelled pumpkin seeds with an egg white, allulose (see notes under low carb sweeteners regarding this product), and some more of the pumpkin spice. Mix until everything is coated and add about a tablespoon of the mixture to the top of each muffin.

Keto pumpkin muffin topping, keto candied nut mixture.

Bake the larger muffins for roughly 25 minutes. They will rise a bit and set along the sides. Use a toothpick to check that it comes out clean and let them cool slightly before pulling from the pan.

Nutritional information may vary based on what low carb sweeteners you use and what size muffins you make, the listed information below is for standard size muffins.

Keto Pumpkin Muffins, baked in the muffin tin.

Serving and Storing-

I love digging into these muffins where they are warm. They store for up to seven days in a container on the counter as needed and also freeze well individually. Warm one up for 15 seconds in the microwave and enjoy with your morning coffee.

Keto Pumpkin Muffins being held by a hand.

If you’d rather make an optional icing for these muffins with cream cheese or low carb powdered sweetener, check out the glaze recipe I have with these keto pumpkin bread scones as a guide.

Not ready to make this recipe, but want to save it for later? Pin this to Pinterest or bookmark to you desktop!

Looking for other pumpkin recipes? Give these keto pumpkin hand pies, low carb pumpkin pie, and even this keto and gluten free pumpkin pizza recipe a try!

Keto pumpkin muffins on a tray.

The Best Keto Pumpkin Muffins

Master the perfect almond flour pumpkin muffins recipe that will make even the least basic pumpkin lover, swoon. They’re the best light, airy, sugar free and grain free style keto pumpkin bread you will want to make over and over again.
4.95 from 18 votes
Print Pin Rate
Course: Breakfast
Cuisine: American
Keyword: keto pumpkin muffins
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes
Servings: 24 small muffins
Calories: 126kcal
Author: Bon Appeteach


Keto Muffin Batter:

  • 1/2 cup Pumpkin Puree
  • 4 oz. Cream Cheese softened
  • 4 tbsp. Butter softened
  • 1 tsp. Vanilla
  • 2 tsp. Pumpkin Pie Spice
  • 1 cup Low Carb Sweetener
  • 5 Eggs
  • 2 1/2 cup Almond Flour
  • 2 tsp Baking Powder
  • 1 tsp. Salt


  • 1 Egg White
  • 1/4 cup Chopped Pecans
  • 1/4 cup Allulose or other low carb sweetener
  • 2 tbsp. Pepita Seeds
  • 1/2 tsp Pumpkin Pie Spice


  • Preheat the oven to 350 F. Fill a muffin tin with muffin liners.
  • In a stand mixer (or hand mixer), beat together the softened butter, cream cheese, pumpkin puree and low carb sweetener until smooth.
  • Add in the vanilla and pumpkin pie spice and mix again.
  • Next, add in the 5 eggs but one at a time. Mix well in between each egg to help incorporate air.
  • Finish the mixture by mixing in the almond flour, salt, and baking powder. Scrape down the sides as needed.
  • In a separate bowl combine the egg white, allulose, 1/2 tsp pumpkin pie spice, chopped pecans, and pepitas. Mix so everything is coated.
  • Fill the muffin cups 3/4 of the way full. Add a tablespoon of topping to each muffin.
  • Bake for 25-30 minutes or until the centers come out clean for the large muffins. Standard muffins will take 15-20 minutes.
  • Let cool until warm and serve.


Store in a sealed container for up to 7 days. Rewarm for 15 sec. in the microwave to eat warm. Freeze individually as needed!


Serving: 1g | Calories: 126kcal | Carbohydrates: 4g | Protein: 4g | Fat: 11g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 44mg | Sodium: 161mg | Potassium: 40mg | Fiber: 2g | Sugar: 1g | Vitamin A: 971IU | Vitamin C: 1mg | Calcium: 60mg | Iron: 1mg

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Recipe Rating

  1. This recipe is absolutely outstanding! So delicious! I can finally say I’ve found a replacement for the carb filled pumpkin bread my mom and I used to bake by the dozens over the holiday!

  2. These really do look like the BEST keto pumpkin muffins for fall!! We can’t wait to try making them ourselves! With every recipe that L comes out with, she proves that Bonappeteach is THE place to find the hottest, tastiest, and healthiest keto recipes around!! Can’t wait for your next recipe, L!

    Your Canadian BBQ sisters,
    Maddie & Kiki

  3. Delicious. I just had my first bite. Can’t tell it’s a low-carb muffin. I do have a question regarding the topping. Is it supposed to be a tsp. and not a Tbsp. per muffin? Doing the math, it doesn’t work as stated. Needless to say my last dozen were quite skimpy on the topping.

    1. Hi Lynn,

      Thanks for sharing your feedback! It may depend on how chopped your nuts are? Also, while I tested the smaller batch muffins, I never tested the topping for them. You would however not need as much for a smaller muffin in theory, so I will make some notes and adjustments to limit confusion. I really appreciate you sharing your experience. Happy cooking! -L