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BEST Keto Pumpkin Muffins with Cream Cheese Swirl

These Keto Pumpkin Muffins have a delicious cream cheese swirl making them moist, flavorful, and full of pumpkin spice goodness. My low carb pumpkin muffins make for the perfect breakfast or snack. They are easy, and a great option for those who are on a low carb diet or gluten-free.

Easy Keto Pumpkin Muffins

It’s that glorious time of year again….FALL!!! In case you didn’t know fall is my absolute favorite time of year. The weather is changing, our mornings and nights are crisp while the days are still sunny and warm. I’m pulling out my sweaters, and leggings but do you know that else I’m doing? This is the season for everything pumpkin, and we’ve been baking up a storm. 

Today we’re going to share with you our new recipe for keto pumpkin muffins. If you have tried our Pumpkin Chocolate Chip Muffins and loved them, then I think you are going to love these ones too. 

What makes these low carb pumpkin muffins even better than just plain pumpkin muffins is that they are low carb pumpkin cream cheese muffins…that’s right they have cream cheese in them! Well, to be exact it’s a cream cheese swirl, and they are swirled to perfection. 

If you are as big of a fan for the fall time and love pumpkin then please try our Pumpkin Chocolate Chip Cookies, Keto Pumpkin Pie, Low Carb Pumpkin Bread, and more.

What are Pumpkin Muffins?

What are pumpkin muffins exactly? They are like all your other classic muffins, but they have canned pumpkin and some homemade pumpkin pie spice…then baked to perfection! They are moist inside, super flavorful and a great breakfast option or dessert.

The Cream Cheese Swirl is Key!

OH…did I mention that I added a cream cheese swirl on top?! It’s the bomb diggity…sorry I regressed back to my teen years. But in all seriousness, the cream cheese swirl is not only key to these low carb pumpkin muffins, but it just takes them to another level. Trust me, they are delicious!

Are Pumpkin Muffins Healthy?

Keto Pumpkin Muffins with cream cheese swirl

These Keto pumpkin spice muffins are actually pretty light, they are low in calories per muffins and that’s including the cream cheese swirl. A lot of muffins that you will find in bakeries and different donut shops are not going to be the healthiest option, contrary to what you may think. 

I want to show you the comparison: 

  • 1 Dunkin Donuts Pumpkin Muffin – 550 calories!!
  • 1 of our Keto Pumpkin Spice Muffins – 152 calories!! 

That means that technically you can eat 3 of our muffins and it will still be fewer calories than 1 pumpkin muffin from Dunkin. Crazy right?

Are Pumpkin Muffins Keto-Friendly? 

I’m so happy to share these keto-friendly pumpkin muffin recipe with you. “Keto-friendly” being the important wording here. They are low carb and keto-friendly because of their low NET Carb count due to being made with almond flour and coconut flour, and a keto-friendly sweetener.

 Let’s go back to comparing our low carb pumpkin muffins and Dunkin Donuts pumpkin muffins. 

  • 1 Dunkin Donuts Pumpkin Muffin – 75 NET CARBS…WHOA!
  • 1 of our Keto Pumpkin Spice Muffins – 3.1 NET CARBS!!!

What Ingredients are in Low Carb Pumpkin Muffins?

Keto Pumpkin Muffins ingredients

MUFFINS:

  • Almond Flour
  • Coconut Flour 
  • Eggs 
  • Low Carb Sweetener – Powdered Swerve
  • Pumpkin Puree – Canned pumpkin….not pumpkin pie filling 
  • Almond Milk – Unsweetened almond milk 
  • Pumpkin Pie Spice – Try our homemade pumpkin pie spice
  • Baking Powder 
  • Baking Soda 
  • Salt 
  • Vanilla 

CREAM CHEESE SWIRL:

Ingredients for cream cheese frosting
  • Cream Cheese – Softened cream cheese is key 
  • Butter – Also needs to be softened, but not melted
  • Vanilla – I love vanilla, but feel free to go a little less on the vanilla if you want
  • Low Carb Sweetener – Powdered Swerve 
  • Heavy Cream – 2 tablespoons

Using Almond Flour and Coconut Flour for Keto Pumpkin Muffins

Like a few of my other muffin recipes, I chose to use a combo of both almond flour and coconut flour. I really have been happy with all of my different muffin recipes that have the combo. 

The majority of the recipe is almond flour, and then just about 2 tablespoons of coconut flour. 

If you want to omit one or the other, you can use just almond flour or just coconut flour to make these low carb muffins. 

  • If you chose to just use almond flour then up the amount from 2 cups to 2 ½ cups. 
  • If you want to use just coconut flour, then you need far less coconut flour than you would almond flour. You need about ½ cup coconut flour to make these muffins. I haven’t tried them personally but everyone who makes coconut flour muffins say that you will get about 6-8 muffins when using ½ cup of coconut flour. 

If you are unsure which brands of almond flour or coconut flour to buy, because there are several out there, here are my 2 favorites:

  • Almond Flour: Kirkland Signature Superfine Almond Flour 3lb bag. It’s about $13.00, which is a great price! Per ¼ cup it has 5g carbs and 3g fiber.
  • Coconut Flour: Organic Bob’s Red Mill Coconut Flour 1lb bag. Per 2 tbsp has 9g carbs and 5g fiber.

Butter vs. Coconut Oil

I actually don’t use butter or oil for these Keto pumpkin muffins. I suppose you could use them, but I found that the recipe really doesn’t need either.

Fresh Pumpkin vs Pumpkin Puree for Muffins

pumpkin puree and eggs for Low Carb Pumpkin Muffins

I always recommend using canned pumpkin puree for best results instead of using fresh pumpkin. Just make sure that your canned pumpkin is 100% pumpkin, and there aren’t any added ingredients.

Not only do I prefer the texture of canned pumpkin, but it’s also so so easy. Simply open the can and there you go…pumpkin puree!

If you want to use fresh pumpkin that’s ok, just be careful with the consistency. Fresh pumpkin tends to have a thinner consistency and can be watery, which will alter the texture of your keto pumpkin bread and leave it soggy.

Don’t use pumpkin pie filling…that is full of sugar and added ingredients.

Sweetener Options

I used powdered Swerve in this keto pumpkin muffin recipe. I feel that it blends in very nicely with all the other ingredients and doesn’t leave a gritty taste. 

If you don’t have any low carb powdered sweetener, you can use either granulated monk fruit or any other granulated keto-friendly sweetener. 

I have never used liquid stevia in any of my baked goods, but I know a lot of people do. According to my research, 1 teaspoon of liquid stevia is equivalent to 1 cup sugar. 

I haven’t tried using liquid stevia with these muffins, but if you do please let me know how it comes out. I’d love to know in the review section!

Can I Substitute the Eggs?

I have not tried using an egg replacer in these keto pumpkin cream cheese muffins, but we have in others. 

For those of you who do not eat eggs, chia eggs and flaxseed eggs work well as egg replacements. 

In case you don’t know what either of these are, I’ll quickly tell you. 

1 Flaxseed Egg: 

  • 1 tbsp flaxseed meal
  • 2.5 tbsp water

Mix together, and let sit for 5 minutes until it thickens. 

1 Chia Egg:

  • 1 tbsp chia seeds, or chia seed meal
  • 3 tbsp water

Mix together, and let sit for 5 minutes until it thickens.

Don’t Forget the Pumpkin Spice

Pumpkin Pie Spice recipe

I believe in adding pumpkin spice to pretty much every single pumpkin recipe I make. But I don’t buy pumpkin spice in the grocery store, it’s expensive for a tiny little bottle, and sometimes they even add extra ingredients that we don’t need at all. 

So instead I make my own homemade pumpkin spice. I buy all my ingredients from Costco and I make up a container and keep it in my spice cabinet. 

It even makes for a great gift to your friends and family. I actually made a huge batch last fall, put them in nice glass containers, and gave them to several of my friends. They loved it! 

So check out our recipe for Homemade Pumpkin Pie Spice…it’s a combo of cinnamon, ginger, nutmeg, allspice, and cloves. It screams fall time!

Tools to Use

You don’t need a lot of tools to make pumpkin muffins with almond flour. Here’s all you need:

  • Mixing Bowl
  • Measuring Cups and Spoons
  • Whisk and Spatula
  • Muffin Pan 
  • Muffin Liners 
  • Cooling Rack (optional, but helpful)

Different Variations of Keto Pumpkin Muffins

Keto Pumpkin Muffins with almond flour

There are some different variations we can make to our easy keto pumpkin muffins with cream cheese swirl. For instance: 

  • Leave out the cream cheese swirl.
  • Add chopped walnuts or pecans.
  • Add sugar-free chocolate chips.
  • Instead of a cream cheese swirl, you can add a cream cheese icing after they are cooked.
  • Crumble topping: 2 tbsp softened butter, ¼ cup brown sugar swerve, 2 tbsp coconut flour, 3 tbsp chopped pecans or walnuts, and 1 tsp cinnamon.

How to Make the BEST Keto Pumpkin Muffins

Let’s whip up a batch of these delicious keto pumpkin muffins with cream cheese swirl. Follow these easy instructions. 

Mixing the Batter

STEP 1: Preheat the oven to 350 degrees. 

STEP 2: Start off with our dry ingredients. In a bowl combine the almond flour, coconut flour, powdered Swerve, baking powder, salt, and pumpkin pie spice. Stir together, making sure to get all the lumps out. 

STEP 3: In another bowl whisk the eggs, pumpkin, and vanilla. Whisk the ingredients together.

Add in the almond milk and whisk again.

STEP 4: Add in about ½ of the dry ingredients to the pumpkin mixture, and whisk together. Add in the remaining dry ingredients. I do it this way because it’s easier to get all the ingredients combined.

Baking the Muffins

STEP 5: Place the muffin liners in the pan. Lightly spray the liners with a cooking spray, I found that it helps the muffins from sticking to the liners.

baking tray with muffin liners and Pam

STEP 6: Use a cookie scoop and fill the muffin liners about ¾ of the way full.

Making the Cream Cheese Swirl

IMPORTANT –  Please make sure that your cream cheese is softened otherwise, it will not be the right texture.

STEP 7: In a small bowl combine the cream cheese, powdered Swerve, heavy cream, and vanilla. Whisk together until very smooth.

STEP 8: Now take a ½ tsp and put a little dollop on top of each muffin.

adding sugar free frosting to pumpkin mixture

STEP 9: Using a toothpick swirl the cream cheese into the muffin batter.

How Long to Bake Pumpkin Muffins?

STEP 10: Place the low carb pumpkin muffins into the oven and bake for 25 minutes. In my oven 25 minutes was perfect!

Keto Pumpkin Muffins baking in the oven

Use a toothpick or knife to make sure they are cooked. Keep in mind that the cream cheese swirl will still be pretty soft even after the muffin is cooked.

Low Carb Pumpkin Muffins in a tray after baking

How to Make Low Carb Pumpkin Muffins without Cream Cheese Swirl

If you don’t like cream cheese, you still can enjoy these amazing coconut flour pumpkin muffins. My mom doesn’t often eat cream cheese so she makes them without the swirl and loves them! The muffin is very moist and flavorful on its own. 

So if you are dairy-free, leave out the cream cheese swirl and enjoy a special fall treat.

Making Mini Keto Pumpkin Muffins with Almond Flour

It’s easy to make these into mini low carb pumpkin cream cheese muffins, a great snack idea!

  1. Make the batter the exact same way as the normal ones. 
  2. Grab your mini muffins pan and mini muffin liners. Place the liners in the mini muffin pan. 
  3. Add batter to the liners.
  4. If you choose to add the cream cheese swirl then add ⅛-¼ tsp to each mini muffin. 
  5. Bake for 10-15 minutes instead of the normal 25 minutes since they cook more quickly.

Best Tips

Easy Keto Pumpkin Muffins

I actually don’t have too many tips to share for this recipe but here a few: 

  • If you are dairy-free or don’t like cream cheese, leave it out. The muffins are delicious on their own.
  • Use canned pumpkin or fresh. Do NOT use Pumpkin Pie Filling – it’s full of sugar. 
  • For Egg Substitution – Use flax seed egg or chia egg.
  • Try our Homemade Pumpkin Pie Spice Recipe.
  • For mini keto pumpkin spice, muffins bake for 10-15 minutes. 
  • Make sure the cream cheese for the swirl is softened to room temperature. 
  • When testing the muffins after 25 minutes, the cream cheese swirl will still be soft but the muffin itself should be cooked. 
  • Let them cool completely before eating otherwise, they can fall apart. 
  • Store in the refrigerator for up to 5 days. 
  • Freeze for up to 2 months.

Keeping Keto Pumpkin Muffins Moist

Don’t over bake the pumpkin keto muffins or they will not come out as moist as they should. Overbaking them will dry them out and leave you with a dry coconut flour pumpkin muffin, which no one wants. 

When you test them in the oven the cream cheese topping will still be very soft but the muffin itself should be cooked. Don’t be fooled by the topping and think they are not cooked.

How to Keep Low Carb Pumpkin Muffins from Falling Apart?

Be sure to let the muffins cool completely before eating them. You may be tempted by the smell and look of them, but try to refrain yourself. If you eat them while still warm they can fall apart easily, especially since the cream cheese swirl makes them very soft on top.

Other Diets This Recipe is Good For

best almond flour pumpkin muffins recipe

Gluten-Free: Pumpkin Muffins with almond flour are completely gluten-free. They are made with almond flour and coconut flour. A great gluten-free snack. 

Dairy-Free: The way the recipe is currently it is NOT dairy-free. But remove the cream cheese swirl, or replace the cream cheese with a vegan cream cheese. Then replace the heavy cream with almond milk, and now you have some dairy-free keto pumpkin spice muffins. 

Vegan: Again the way the recipe is right now is not vegan. But replace the cream cheese with vegan cream cheese, or leave it out altogether. Replace the eggs with either flaxseed eggs. or chia eggs. And instead of the heavy cream use almond milk.

How to Make Paleo Pumpkin Muffins

To make these low carb pumpkin muffins paleo, then all you need to do is leave out the cream cheese swirl. Obviously, cream cheese is not paleo so it needs to be eliminated.

Making Dairy-Free Pumpkin Muffins

We can easily make this keto pumpkin muffin recipe dairy-free. 

Option 1: Remove the cream cheese swirl. Not a big deal…they will still taste great. 

Option 2: Replace the cream cheese with vegan cream cheese, and the heavy cream with almond milk.

How to Serve Keto Pumpkin Muffins

Keto pumpkin muffins with cream cheese swirl

Well for starters, there isn’t anything much better than the best keto pumpkin muffins with cream cheese swirl, served alongside a nice hot cup of coffee. 

It’s a great breakfast recipe to be served with some Keto Corned Beef Hash, Egg White Cups, Keto Chaffles, or if you’re looking for a super quick breakfast enjoy these coconut flour pumpkin muffins with a Keto Smoothie.

How to Store Pumpkin Muffins 

I always get nervous with desserts that have cream cheese in them so I air on the side of caution. I store my leftover low carb pumpkin cream cheese muffins in the refrigerator. I either place them in a large Ziploc bag or in an air-tight container. 

They will last up to 5 days if stored properly.

How to Reheat

If you froze these keto pumpkin cheesecake muffins you obviously need to thaw them out before eating them. To thaw place them in the refrigerator overnight, or place on the counter to thaw. 

Then to reheat, place the thawed almond flour pumpkin muffins on a plate and heat in the microwave for about 30 seconds.

Can You Freeze Pumpkin Muffins?

You can absolutely freeze your leftover keto-friendly pumpkin muffins! I like making a batch and having extra muffins leftover. Place them in an air-tight, freezer-safe container and freeze them for up to 2 months.

Keto Pumpkin Muffins Recipe

Low Carb Muffin Recipes

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

Keto Banana Muffins stacked on top of each other

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

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Keto Pumpkin Muffins

BEST Keto Pumpkin Muffins with Cream Cheese Swirl


  • Author: Stephanie Parlegreco
  • Prep Time: 10 minutes
  • Cook Time: 25 minutes
  • Total Time: 35 minutes
  • Yield: 14 Servings (1 Muffin Per Serving) 1x
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Description

These Keto Pumpkin Muffins have a delicious cream cheese swirl making them moist, flavorful, and full of pumpkin spice goodness. Our low carb pumpkin muffins make for the perfect breakfast or snack. They are easy, and a great option for those who are on a low carb diet or gluten-free.


Ingredients

Scale

Muffins

  • 2 cups almond flour
  • 2 tbsp coconut flour 
  • 4 eggs
  • 1 cup powdered Swerve 
  • ¾ cup canned pumpkin
  • ½ cup almond milk
  • 2 tsp pumpkin pie spice 
  • 1 tbsp baking powder
  • ½ tsp salt 
  • 1 tsp vanilla 

Cream Cheese Swirl 

  • 2 oz softened cream cheese
  • ½ tsp vanilla 
  • 1 ½ tbsp powdered swerve
  • 1 tbsp heavy cream

Instructions

Notes

3.1 NET CARBS PER MUFFIN 

If you are dairy-free or don’t like cream cheese, leave it out. The muffins are delicious on their own.

Use canned pumpkin or fresh. Do NOT use Pumpkin Pie Filling – it’s full of sugar. 

For Egg Substitution – Use flax seed egg or chia egg.

Try our Homemade Pumpkin Pie Spice Recipe.

For mini keto pumpkin spice, muffins bake for 10-15 minutes. 

Make sure the cream cheese for the swirl is softened to room temperature. 

When testing the muffins after 25 minutes, the cream cheese swirl will still be soft but the muffin itself should be cooked. 

Let them cool completely before eating otherwise, they can fall apart. 

Store in the refrigerator for up to 5 days. 

Freeze for up to 2 months.

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

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