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    Home » Muffins & Scones » Keto Pumpkin Muffins

    Published: Aug 31, 2022 by Carolyn

    Keto Pumpkin Muffins

    This post may contain Amazon or other affiliate links. As an Amazon Associate I earn from qualifying purchases.

    64.5K shares
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    Try these delectable keto pumpkin muffins with a rich gooey cream cheese center. They’re a delicious fall breakfast or snack. So good that you might even want to eat them for dessert!

    Top down image of a white muffin pan filled with Keto Pumpkin Muffins.

    You don’t want to mess with perfection. Take these keto pumpkin muffins, for example. I first posted this recipe back in 2013 and they were a huge hit from the get-go. Readers love them, and my family does too. So we make them every fall.

    It’s one of my most popular keto muffin recipes, and with good reason. They have that classic pumpkin spice flavor, with a gooey, creamy cheesecake center. No one can believe they’re sugar free.

    They are, of course, modeled after the famous pumpkin muffins from Starbucks. And they taste just as delicious, but with a mere fraction of the carbs.

    How does that sound to you, pumpkin lovers???

    A pan of keto pumpkin muffins filled with cream cheese.

    Why you must try this recipe

    In case you haven’t noticed, I am a huge fan of keto pumpkin recipes. There is something so lovely and comforting about the warm spices paired with pumpkin puree.

    And these muffins are no exception. They are tender and sweet, with hints of cinnamon, ginger, and cloves. And that sweet cheesecake center takes them to the next level. But if you prefer them plain, I offer instructions for that too!

    Best of all, these keto pumpkin muffins have only 3.7g net carbs per serving. Compare that to the hefty 53g of carbs in the Starbucks version.

    Other fan favorites include my Keto Pumpkin Cream Pie and Easy Pumpkin Breakfast Bars. And let me not forget my updated Keto Pumpkin Bread, which gets rave reviews every time!

    A keto pumpkin muffin broken open on a white plate to show the cream cheese filling.

    Reader Testimonials

    “I made these exactly as written. They were easy to make and tasted fabulous! I can always count on your recipes to be delicious!” — Dana

    “These are pure perfection, so delicious! I like extra simple recipes with standard ingredients, and even with the a separate filling, these are simple enough for me to put in regular rotation. I just need to remember to make a double batch next time. Thank you!” — Jamie

    “These muffins are the VERY BEST thing I’ve made using Keto ingredients! Thanks!” — Kathy

    Ingredients you need

    Top down image of ingredients for keto cream cheese filling.

    Cream Cheese Filling:

    • Cream cheese: Use full fat cream cheese as low fat cream cheese has fillers that can make it higher in carbs.
    • Powdered Swerve Sweetener: Use a powdered sweetener for the cream cheese filling so there’s no residual grittiness.
    • Heavy cream
    • Vanilla extract
    Top down image of ingredients for Keto Pumpkin Muffins

    Pumpkin Muffins:

    • Almond flour: Choose a good, finely ground almond flour for the best texture. This recipe won’t work well with coconut flour, but you can use sunflower seed flour for a nut-free version.
    • Swerve Brown: A brown sugar replacement is ideal for the best keto pumpkin muffins. But any granular sweetener should be fine in these, so use what you like best. Do be aware that allulose will make them brown much faster.
    • Unflavoured whey protein powder: It’s important to understand the science behind keto baking. Gluten is a protein and in its absence, another dry protein helps baked goods rise properly. You can skip the protein powder, but your muffins will be more dense and fragile. You can also use egg white protein powder instead.
    • Pumpkin pie spice: If you don’t have pumpkin pie spice, you can combine ground cinnamon, ginger and cloves.
    • Pumpkin purée: You can use homemade or canned pumpkin purée. If it’s on the thinner side, reduce the amount of added liquid.
    • Pantry staples: Eggs, butter, baking powder, salt and vanilla extract.

    Step-by-step directions

    A collage of 6 images showing the steps for making keto pumpkin muffins.

    1. Prepare the filling: Beat the cream cheese with the powdered sweetener, cream and vanilla extract until smooth. Set aside.

    2. Whisk the dry ingredients: In a medium bowl, whisk together the almond flour, sweetener, protein powder, baking powder, pumpkin pie spice, and salt.

    3. Stir in the wet ingredients: Add the eggs, pumpkin puree, melted butter, water, and vanilla extract. Mix until well combined.

    4. Fill the muffins: Line a muffin tin with parchment or silicone liners. Drop a spoonful of batter into the bottom of each and use a spoon to make a well in the center. Drop a tablespoon of the filling into the well, then top with more batter to cover.

    5. Bake the muffins: Bake at 325F for 23 to 25 minutes, or until the tops are set and the edges are browned. Let cool in the pan.

    A stack of keto pumpkin muffins in front of two felt pumpkins.

    Expert tips

    The filling is optional! I have made these keto pumpkin muffins several different ways. I love the filled muffin style, but I have also swirled the cream cheese into the top of the batter (very pretty!). And I’ve made them with no filling at all!

    So if you prefer a classic pumpkin muffin, feel free to skip the filling. Adding chopped nuts or chocolate chips is delicious too.

    The rise and fall of keto pumpkin muffins: If you do make filled muffins, expect them to rise nicely and then sink a bit as they cool. That is the nature of cream cheese stuffed goodies. The filling expands during baking, and then contracts as it cools. So a little sink hole will appear in the tops of the muffins. They still taste fabulous!

    Dairy-Free Option: You can make these muffins dairy-free as well, with egg white protein powder, dairy-free cream cheese, and coconut cream. Replace the butter with your oil of choice and enjoy!

    Keto Pumpkin Cream Cheese Muffins on a white cake platter.

    Frequently Asked Questions

    Is pumpkin puree keto?

    Canned pumpkin puree has 12g of carbs and 4g of fiber per half cup serving. While it’s not the lowest carb option, it can be consumed on a keto diet in small quantities. This keto muffin recipe uses only half a cup spread out over 12 servings, so it’s very keto-friendly.

    How many carbs are in keto pumpkin muffins?

    This keto muffin recipe has 6.1g of carbs and 2.4g of fiber per serving. That comes to 3.7g net carbs per muffin.

    What can I use instead of almond flour?

    This keto pumpkin muffin recipe was developed and tested using almond flour. However, you can use sunflower seed flour as a 1 to 1 replacement. Just remember to add a tablespoon of lemon juice to offset the reaction between sunflower seeds and baking powder. They will turn a lovely shade of green if you forget!

    Two keto pumpkin muffins on a white plate with a cup of coffee behind.

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    A keto pumpkin muffin broken open on a white plate to show the cream cheese center.

    Keto Pumpkin Muffins Recipe

    Delectable keto pumpkin pumpkin muffins with a rich gooey cream cheese center. They're a delicious fall breakfast or snack. So good that you might even want to eat them for dessert!
    4.31 from 109 votes
    Print Pin Rate
    Course: Breakfast
    Cuisine: Brunch
    Keyword: keto pumpkin muffins
    Prep Time: 20 minutes
    Cook Time: 25 minutes
    Resting Time: 15 minutes
    Total Time: 1 hour
    Servings: 12 muffins
    Calories: 221kcal

    Ingredients

    Cream Cheese Filling:

    • 6 oz cream cheese softened
    • 3 tablespoon powdered Swerve Sweetener
    • 1 tablespoon heavy cream
    • ½ teaspoon vanilla

    Pumpkin Muffins:

    • 2 cups almond flour
    • ½ cup Swerve Sweetener
    • ¼ cup unflavoured whey protein powder (or egg white protein)
    • 2 teaspoon baking powder
    • 2 teaspoon pumpkin pie spice (Or 1 teaspoon cinnamon, ½ teaspoon ginger, ¼ teaspoon cloves)
    • ½ teaspoon salt
    • 2 large eggs
    • ½ cup pumpkin puree
    • ¼ cup butter melted
    • ¼ cup water
    • ½ teaspoon vanilla extract
    US Customary – Metric

    Instructions

    Cream cheese filling

    • Beat the cream cheese with the powdered sweetener, cream and vanilla extract until smooth. Set aside.

    Muffins:

    • Preheat the oven to 325ºF and line a muffin tin with parchment or silicone liners.
    • In a medium bowl, whisk together the almond flour, sweetener, protein powder, baking powder, pumpkin pie spice, and salt.
    • Add the eggs, pumpkin puree, melted butter, water, and vanilla extract. Mix until well combined.
    • Drop a spoonful of batter into the bottom of the prepared muffin tins and use a spoon to make a well in the center of each. Drop a tablespoon of cream cheese filling into the well, then top with more batter to cover.
    • Bake 23 to 25 minutes, or until the tops are set and the edges are just browned. Let cool completely in the pan.

    Notes

    Variations:

    Swirled Pumpkin Muffins: Instead of filling the muffins, swirl the cream cheese into the batter top of the batter. Bake as directed. 
    Plain Pumpkin Muffins: Fill the muffin cups with the batter and bake 15 to 20 minutes. They will bake faster than those with cream cheese. You can also add chocolate chips or chopped nuts. 

    Storage information:

    Store the muffins in a covered container on the counter for up to 3 days or in the fridge for up to 7 days. They can also be frozen for several months. 
    Nutrition Facts
    Keto Pumpkin Muffins Recipe
    Amount Per Serving (1 muffin)
    Calories 221 Calories from Fat 166
    % Daily Value*
    Fat 18.4g28%
    Carbohydrates 6.1g2%
    Fiber 2.4g10%
    Protein 7.5g15%
    * Percent Daily Values are based on a 2000 calorie diet.

     

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    Nutritional Disclaimer

    Please note that I am not a medical or nutritional professional. I am simply recounting and sharing my own experiences on this blog. Nothing I express here should be taken as medical advice and you should consult with your doctor before starting any diet or exercise program. I provide nutritional information for my recipes simply as a courtesy to my readers. It is calculated using MacGourmet software and I remove erythritol from the final carb count and net carb count, as it does not affect my own blood glucose levels. I do my best to be as accurate as possible but you should independently calculate nutritional information on your own before relying on them. I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.

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      Recipe Rating




    1. Zana says

      February 22, 2023 at 2:46 pm

      5 stars
      Made them last night and another batch for freezing today…. Love them!! Thank you for sharing the recipe!

      Reply
    2. Jyl says

      February 05, 2023 at 7:17 pm

      5 stars
      WOW! I am blown away by the texture and wonderful flavor of these muffins! Easy to make, easy to bake, and almost too easy to eat! Each one is an adventure on the pumpkin spice side of things, which even in February is mighty tasty and satisfying. Thank you for sharing this recipe!!!

      Reply
      • Carolyn says

        February 07, 2023 at 5:08 pm

        Glad you enjoyed them!

        Reply
    3. Cheryl says

      January 17, 2023 at 7:08 pm

      5 stars
      so with the price of eggs I just couldn’t use your regular pumpkin bread recipe, Soni took the muffins and made it into bread.. delicious

      Reply
    4. Lisa Gray says

      November 15, 2022 at 7:27 pm

      5 stars
      I made these today, and they are fantastic! I wouldn’t know they were keto or sugar free if I hadn’t made them myself.!

      Reply
    5. Kari says

      November 09, 2022 at 7:56 am

      Would a cinnamon flavored protein powder work ok?

      Reply
    6. Lilly says

      November 08, 2022 at 1:06 pm

      5 stars
      They turned out great, but I’ve got to tell you, after the muffins were done, I opened the microwave only to find the butter still sitting in there, oops!
      I can’t wait to try these again but WITH the butter. Thanks

      Reply
      • Carolyn says

        November 08, 2022 at 10:26 pm

        Well… so glad they stilled turned out!

        Reply
    7. KT says

      October 30, 2022 at 11:15 am

      5 stars
      SO good! Since I didn’t have powdered sweetener, I mixed the cream cheese with 2 T keto maple syrup and omitted the cream and vanilla. It tasted great straight out of the bowl, so I was confident this was a good (and easy!) swap. I made them into mini muffins for finger food at our football tailgate, and I pressed 3-4 chocolate chips into the top of each before baking. I got compliments from friends and strangers, and these are my new favorite fall treat! Excellent recipe, thanks so much for sharing!

      Reply
    8. Annette says

      October 24, 2022 at 3:22 pm

      5 stars
      I made these this morning and they were delicious! My husband enjoyed them too. I highly recommend this recipe.It’s perfect for this time of year. Note: I didn’t have any whey protein so I used dry vanilla protein shake instead and they were still very tasty but a bit moist.

      Reply
      • Carolyn says

        October 25, 2022 at 8:40 am

        Thank you!

        Reply
    9. Kate says

      October 16, 2022 at 11:29 am

      5 stars
      These muffins blew me away. Just like a gluten/sugar full muffin. The crumb is amazing! The egg white powder made the texture so good and just like the real thing. Thank you for this recipe!

      Reply
    10. John says

      October 13, 2022 at 3:52 pm

      5 stars
      These are incredible! The cream cheese center rocks???? I mached this with a keto toffee iced coffee (say that 3 times fast!????) for a ????fall afternoon treat! What a winner!!

      Reply
    11. Sharon says

      October 11, 2022 at 4:26 pm

      Can I use whole egg powder from auguson farms as a sub for whey protein powder

      Reply
      • Carolyn says

        October 11, 2022 at 5:23 pm

        I don’t believe that would work that well.

        Reply
    12. Beatrice Williams says

      October 10, 2022 at 6:47 am

      5 stars
      I made these and delish!!! Type 2 diabetic here. Keto 2 years. I am healthier than I have ever been on keto and avoided insulin with this lifestyle!! Keto onwards sister!!; Love your recipes!!!

      Reply
    13. Becky says

      October 09, 2022 at 7:26 pm

      5 stars
      Really yummy! I intended to swirl the cream cheese in, but it was too thick, so I just kind of pressed it down. I was afraid it might brown too much, but it did not. They baked up beautifully and were a real treat hot from the oven, with the cream cheese warm and melty. I bet they’ll be just as good chilled.

      Reply
    14. Sue says

      October 07, 2022 at 9:37 am

      5 stars
      These are delicious!

      Reply
    15. Beatrice Williams says

      October 07, 2022 at 8:04 am

      5 stars
      I made these muffins and they are perfection!!! When I also swirled the cream cheese on top they seemed to brown lighter in color…I love that golden thing going on!!! I love the fall and this recipe just tips it off!!!

      Reply
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