Low Carb Pumpkin Cream Cheese Cupcakes, Need I say more?

A delicious low carb keto friendly pumpkin cream cheese cupcake recipe.

Yup, I did it again! I couldn’t resist making yet another low carb pumpkin recipe. Can you blame me though? I mean really who does not love pumpkins?

Oh, I guess there is that rare soul out there, but we forgive you. Honestly, there is just something about this time of year that makes me want to make as much pumpkin goodness as possible. Am I the only one who feels this way?

When I started out to create this recipe I wanted the pumpkin and spices pronounced, so that’s why you will notice I added a good dose of pumpkin spice.

If you’re not that much of a fan, by all means, lower the amount. Although, I have no idea why you would ever want to tinker with this recipe.

The only thing instead of whipped cream that these delights can use is a low carb cream cheese frosting. So I went ahead and added my recipe for this too just to make your grin larger. Make sure you remember to also check out our Keto Cream Cheese Recipes.

Please share with me if you too love all things pumpkin. Not a fan? Well, please try to make the rest of us understand.

Eating low carb means I have to get a little creative when it comes to making this season’s favorite treats. I don’t want to eat something that will kick me out of ketosis.

Low Carb Pumpkin Cream Cheese Cupcakes

Low Carb Pumpkin Cream Cheese Cupcakes, Need I say more?

Yields 24

10 minPrep Time

30 minCook Time

40 minTotal Time

Save RecipeSave Recipe


    Pumpkin cupcake batter
  • 12 oz cream cheese, softened (1 ½ packages)
  • 8 eggs
  • 2 cups of sugar substitute (I used swerve)
  • 1 ½ cups of golden flax meal
  • 15 oz can pumpkin puree
  • 3 tsp pumpkin pie spice
  • 2 tsp cinnamon
  • 2 tsp of baking powder
  • ¼ tsp of salt
  • ¼ tsp lemon extract (can substitute for vanilla)
  • Cream Cheese Frosting (optional)
  • 8 ounce package of softened cream cheese
  • 1/2 stick (1/4 cup)of unsalted butter softened
  • 1 cup of heavy whipping cream
  • 1 cup of sugar substitute
  • 2 tablespoons of Swerve sugar confectioners substitute (to dust the tops of the cupcakes (optional)


    Low Carb Cream Cheese Frosting
  1. Beat the cream cheese and butter until light and fluffy in a stand-up mixer.
  2. Next add the heavy whipping cream and beat until fully combined.  
  3. Filling
  4. Add the sugar substitute one tablespoon at a time gently mixing so as to not lose too much volume.
  5. Pre-heat oven to 350 degrees.
  6. Line two 12 muffin tin pans with muffin liners.
  7. Beat the cream cheese in a large electric mixture.
  8. Add the 8 eggs one at a time, combining well after each addition.
  9. Next add the rest of the ingredients until fully combined. Note that the batter will be thick, this is normal.



4411 cal


364 g


204 g


104 g
Click Here For Full Nutrition, Exchanges, and My Plate Info

Nutrition Facts
Serving Size 1 cupcake
Servings Per Container 24

Amount Per Serving
Calories 176 Calories from Fat 139.5
% Daily Value*
Total Fat 15.5g 24%
Saturated Fat 7.7g 39%
Trans Fat 0g
Cholesterol 91mg 30%
Sodium 91mg 4%
Total Carbohydrate 5g 2%
Dietary Fiber 2.4g 10%
Sugars 0.8g
Protein 5.5g 11%

*Percent Daily Values are based on a 2,000 calorie diet. Your daily values may be higher or lower depending on your calorie needs.






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  1. Yummmmm!!! Pumpkins make me smile :)
  2. I haven't tried cooking with flaxseed meal. What are your thoughts?
    • Hi Lucy, I don't mind the flavor or texture. What I have learned is to make sure it is fully baked because it tends to take longer when baking. I also usually add lots of spices because some people don't care for the taste. The best part of using flax meal is that it's very inexpensive. I use it as a sub for hot oatmeal, since oatmeal has too many carbs for my taste. I just add a few spoonfuls to a cup of hot water and then a little creamer and sugar sub. It's a great winter treat. ?
      • What sugar substitute are you basing the amounts on? I am doing Trim Healthy Mamas and there are types of substitutes where 1 cup of sugar substituted can be a different measurement for each sweetener. Does that make sense?
      • Hi Jan, I use several, either stevia that has a bulking agent, Splenda with a bulking agent or swerve which is erythritol a sugar alcohol. Erythritol isn't as sweet and some people prefer to add 1/4 cup more. In the end all work well. Enjoy in good health! I believe trim healthy mama has their own baking sugar substitute that I hear is also very good. I have but I have not tried it yet. ?
      • Hi Jan, I located a free and easy recipe builder. It's sparks people recipe calculator. Google this and it will take you there. I hope this helps. I am going to use it myself. ?
  3. Hahaha I love you Hilda ? why are you doing this to me! ? I want pumppppkins!!!
  4. Yum! Thanks for these posts! :)
  5. i am a lover of all things pumpkin and these sound and look delicious! What are you using for your sugar substitute?
  6. Going to have to try these
  7. Pumpkins and cream cheese = heaven.
  8. deborahcrocker, I love the idea of canning your own pumpkin and I'd love to have instructions for that. Did you create your own recipe or use one you found elsewhere? I would love for you to send me those instructions. I've not done a lot of canning so have no idea how to go about canning pumpkin. I have a pumpkin sitting on my dining room table and my husband has planted more, although they don't seem to be doing very well right now. But I plan on having more next year. I love pumpkin.
  9. Michele, I will have to look that up . I'll get back to ya either today or tomorrow. Lord, help me find this recipe.
    • Thank you deborahcrocker.
      • Michele, I looked in my Ball Blue Book. No recipe. Uh-oh. I put my pumpkin up fall 2013, & could not remember where I got the recipe. So I googled. LOL! Works every time. Check out the site- Simply Canning.com for great instructions. You must have a canning pressure cooker ($65+/- at Wal Mart), not cold water pack canner. And only can in cubes, the pumpkin won't process if puréed. Good luck, let me know how it turns out. Now I might have to get some pumpkin next. Next week I'm planning to can apples, found on sale at 79 cents a pound.
      • Thank you deborahcrocker, for the site. I'll definitely check it out. But I do not have a pressure canner so I will have to get one before I can even think about canning any pumpkin. And I recently bought some apples for 65 cents a pound, sweet price.
  10. Sounds delicious! Love pumpkin season!!
  11. thank you for sharing this YUMMY-looking recipe! i have TONS of butternut squash, which is also naturally sweetish - would that work as a pumpkin substitute, just because they're already "in-house"?? many tx, if you can answer - i'll continue to explore your cool website! :)
  12. Sounds great, but I like to know how many carbs are in one cake . Thank you Dorle
  13. I have two cans of pumpkin purée taunting me in my cupboard... So obviously I HAVE to make these ? Can I sub almond flour for the golden flax??
    • Hi Lauren, yes it will substitute perfectly. Who says pumpkin is only for the fall? Enjoy in good health! ?
      • Made these yesterday for my 5 year old t1d. They are his new favorite! The almond flour worked perfectly. I used swerve which doesn't affect his BS so I only counted carbs in the almost flour and pumpkin, which came to about 6 carbs. I added a few dark chocolate chips to half of the muffins to up the carb count a tiny bit to treat lows. So good! Thanks for sharing!
      • Hi Lauren, Awesome so glad you all enjoyed them. Thanks for sharing your experience. Follow our blog and share ?

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