These Keto Pumpkin Muffins with Cream Cheese are the perfect treat for fall. They feature the irresistible combination of pumpkin spice, tangy cream cheese, and sweet vanilla. These muffins are keto, low-carb, grain-free, and gluten-free!
You know those pumpkin muffins that taste like sweet autumn time? That's these. First, you bite into the pumpkin spice that feels so comforting and warm. Then, the soft cream cheese filling.
It's like a cheesecake and a muffin all in one warm handheld pastry!
If you have a craving for something sweet while you are on keto, reach for these keto pumpkin muffins with cream cheese.
Why You Will Love these Pumpkin Muffins!
- Easy: It takes less than 30 minutes to whip up a batch of these muffins, which are great for breakfast or dessert!
- Low carb: Each muffin contains only 4g of net carbs.
- Perfect for a crowd: This recipe yields 12 muffins so it is a great option to make if you are hosting a brunch or have overnight guests to feed in the morning.
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Ingredients
These are entirely homemade, but most of the ingredients are probably in your kitchen already.
Here's what you'll need before you begin baking these keto muffins.
Pantry Staples
- Almond Flour: A great gluten-free and keto-friendly alternative to all-purpose flour.
- Coconut flour: A dense flour that adds sturdiness to the muffins. If you don't have it on hand, you can sub the 1/4 cup coconut flour for 3/4 cup almond flour.
- Coconut oil: To provide healthy fats and moisture to the muffins.
- Baking powder & baking soda: To help the pumpkin muffins rise when they bake.
- Ground cinnamon, pumpkin pie spice and salt: The perfect spices for that classic pumpkin flavor.
- Xanthan gum: Helps to bind the ingredients together.
- Vanilla extract: Use 100% pure for the best flavor and sweetness.
- Granular erythritol: The keto version of regular sugar.
- Confectioner erythritol: The keto version of powdered sugar.
- Pumpkin puree: This should be pure pumpkin not pumpkin pie filling.
Refrigerated Items
- Almond milk: Make sure it is unsweetened. You can also substitute full-fat coconut milk or heavy cream.
- Butter: Use unsalted softened butter so that it combines easily with the other ingredients.
- Cream cheese: Again, this should be softened and use full-fat.
- Eggs: Use organic and pastured eggs if possible.
How to Make Keto Pumpkin Muffins
The full instructions are detailed in the recipe card at the end of this post.
But we wanted to give you step-by-step instructions, so you know exactly how to make these low-carb pumpkin muffins.
Step #1. Prepare the Muffin Batter
First, mix together the dry ingredients in a large mixing bowl. Next, use an electric mixer (stand or handheld) to beat in the softened butter.
In a separate bowl, beat together the wet ingredients (eggs, coconut oil, pumpkin puree, vanilla extract, and almond milk).
Add the wet ingredients with the dry ingredients and beat once more to fully combine. Your muffin batter will look like the picture below.
Step #2. Make the Cream Cheese Filling
Make your filling by beating together the cream cheese, confectioner erythritol, and vanilla extract until fully combined in a separate medium bowl.
Step #3. Assemble the Muffins
Line your muffin tin with cupcake liners. You need one 12-cavity tin or two 6-cavity tins.
Fill each cupcake liner two-thirds full with the batter (use about 1/4 cup for each one). Don't overfill them and make sure to reserve a cup or so of batter to use later.
Now it's time to assemble the muffins.
Here is a step-by-step on how to do this:
- A) Create a Cavity in the Batter - Use the back of a spoon or your finger to create a crater or small divet in the batter. You want it to be big enough to add in your cream cheese mixture.
- B) Fill the Hole with the Cream Cheese Mixture - Now add in about 1 1/2 teaspoons of the cream cheese mixture into each cavity. Don't use all of it, save some for the topping.
- C) Add the Rest of the Batter - Next, take the rest of the pumpkin batter that you reserved and spoon a small dollop to the top of each muffin. It doesn't have to cover the cream cheese fully.
- D) Top with the Rest of the Cream Cheese Mixture - Now add another tiny bit of the cream cheese mixture on top of the pumpkin batter topping. Use a toothpick to swirl it together.
Step #3. Bake the Muffins
Put the pumpkin muffins in the oven and let them bake for 18-20 minutes at 350°F or until the muffins are golden brown on top.
This is the best part! Your entire house will smell like pumpkin spice!
Recipe Notes and Tips
- Make your own confectioners erythritol. If you don't have this on hand, you can add granular erythritol to a food processor and process until it becomes a powder. It should have the look and feel of powdered sugar.
- Use cupcake liners. This muffin batter is really sticky so we recommend using liners in the muffin tin. Paper, silicone, or foil liners all work.
- Baking times vary. Every oven is different so if the muffins aren't cooked through after 20 minutes, cover the muffin tin with foil (so the tops don't burn) and keep baking the muffins checking them every 5 minutes until they are fully cooked.
- Storage. Store any leftover muffins in a sealed container at room temperature for one day and then store in the refrigerator for up to 7 days after that.
Frequently Asked Questions
Yes, it is (in moderation)! Pumpkin is loaded with fiber, potassium, and vitamin C, which are great for a Clean Keto Lifestyle. However, pumpkin is a squash and it does have carbs in it - approximately 5 grams per ½ cup. So make sure to adjust your serving size accordingly to fit within your macros.
To make you own, you can just combine the following spices together:
4 teaspoons ground cinnamon
2 teaspoons ground ginger
1 teaspoon ground cloves
1/2 teaspoon ground nutmeg
Store this spice mixture in a sealed container at room temperature for up 6 months.
These muffins freeze beautifully. To freeze the muffins, let them cool completely first. Then, wrap them up individually in plastic wrap. Place the muffins in a plastic bag or another freezer container.
Re-heating them is simple. Let them thaw overnight in the refrigerator and then heat them in the oven at 350°F oven for 10-15 minutes.
More Keto Dessert Recipes
If you’d like more delicious desserts that are perfectly keto, then check out these favorites:
- Keto Pumpkin Cake Pops
- Keto Pumpkin Bread Whoopie Pies
- Keto Pumpkin Pie
- Keto Cinnamon Rolls with Brown Butter Icing
- Keto Zucchini Bread Whoopie Pies
We Can't Wait To See You Try It!
We love seeing our recipes come to life!! We can’t wait to see how you make these and loving seeing each person's unique spin on it! Tag us on Instagram @cleanketolifestyle or use the hashtag #CKLrecipe!
Keto Pumpkin Muffins with Cream Cheese
Ingredients
For the Pumpkin Muffin Batter
- 1 1/4 cup almond flour
- 1/4 cup coconut flour
- 1 1/2 teaspoons baking powder
- 1/2 teaspoon baking soda
- 1 teaspoon xanthan gum
- 1 1/2 teaspoons ground cinnamon
- 1/2 teaspoon pumpkin pie spice
- 1/4 teaspoon salt
- 3/4 cup granular erythritol
- 6 tablespoons softened butter
- 2 eggs
- 1/4 cup coconut oil
- 1/2 cup pumpkin puree
- 1 teaspoon vanilla extract
- 2 tablespoons almond milk
For the Cream Cheese Filling
- 8 oz. softened cream cheese
- 1/2 cup confectioner erythritol
- 1 teaspoon vanilla extract
Instructions
For the Pumpkin Muffin Batter
- Heat your oven to 350°F.
- In a large bowl, mix together the almond flour, coconut flour, baking powder, baking soda, xanthan gum, ground cinnamon, pumpkin pie spice, salt, and granular erythritol.
- Use an electric mixer to beat in the softened butter to the dry ingredients until the mixture resembles coarse sand.
- Rinse off your electric mixer beaters.
- In a separate medium bowl, use the electric mixer to beat together the eggs, coconut oil, pumpkin puree, vanilla extract, and almond milk.
- Add this wet mixture into the dry mixture.
- Beat once again until fully combined and set aside.
For the Cream Cheese Filling
- In a separate medium bowl, use an electric mixer to beat together the cream cheese, confectioner erythritol, and vanilla extract until combined and set aside.
To Assemble
- Line a muffin tin with cupcake liners and place about 1/4 cup of batter into each of the 12 liners. (Don't overfill them and reserve about 1/2 cup of the pumpkin batter.)
- Form a hole in the center of each scoop of muffin batter using your finger or the back of a spoon. You want the cavity to be big enough to fill with your cream cheese mixture.
- Fill each hole with roughly 1 1/2 teaspoons of the cream cheese mixture. (Reserve about 1/2 cup of the cream cheese mixture.)
- Take the rest of the pumpkin batter that you reserved and spoon a small dollop (about 2 teaspoons) on the top of each muffin. It doesn't have to cover the cream cheese fully.
- Top each muffin evenly with 2 teaspoons of the reserved cream cheese mixture and use a toothpick or knife to swirl the pumpkin batter into the cream cheese slightly.
- Bake for 18-20 minutes or until the muffins are golden brown on top and cooked throughout.
Notes
- Make your own confectioners erythritol. If you don't have this on hand, you can add granular erythritol to a food processor and process until it becomes a powder. It should have the look and feel of powdered sugar.
- Use cupcake liners. This muffin batter is really sticky so we recommend using liners in the muffin tin. Paper, silicone, or foil liners all work.
- Baking times vary. Every oven is different so if the muffins aren't cooked through after 20 minutes, cover the muffin tin with foil (so the tops don't burn) and keep baking the muffins checking them every 5 minutes until they are fully cooked.
- Storage. Store any leftover muffins in a sealed container at room temperature for one day and then store in the refrigerator for up to 7 days after that.
Mandy
Not sure what I did wrong with these. The flavor is outstanding but I cooked them a good 30 minutes and they never cooked all the way through. They also sank a considerable amount in the middle so they all have large holes in the center. A bummer... After all the ingredients and time.
rachael
has anyone actually made these? I'm so tired of making treats and they turn out horrible. Please comment if you have made them and how they taste!
Jennifer Hubbard
I made these last week and I am about to make more today. My family loved them! They aren't very sweet but have a lovely buttery taste to them . We are cream cheese junkies so we love anything with cream cheese. I didn't notice a much of a pumpkin taste. I may need to add more spices. You can also add more swerve to the batter if you like them sweeter.