Keto Pumpkin Cream Cheese Cupcakes

Keto Pumpkin Cream Cheese Cupcakes

If you’re a fan of pumpkin cupcakes but need a healthier version then this recipe for keto pumpkin cream cheese cupcakes has your name on it.

The good thing is that these Keto Pumpkin Cream Cheese Cupcakes, are low in carbs, grain-free, gluten-free, sugar-free and keto-friendly. Really can it get any better?

I’ve always looked forward to pumpkin season but when I went low carb keto, things had to drastically change. Long gone were the days when I would make a pumpkin recipe oozing with sweetness.

Now that I have learned how dreadful it is to have too much sugar is in our diet, my taste buds no longer crave über sweet foods. Yay for being keto-adapted. It’s pretty remarkable how your body begins to desire less sugar once you remove it from your diet.

I have a complete list of Keto Cakes  that as a fan of cakes I encourage you to also visit. Make sure you remember to also check out our Keto Cream Cheese Recipes.

But this is not to say that I wasn’t craving a pumpkin cupcake. The fact remains that once pumpkin season rolls around this girl gets a major hankering for pumpkin treats. And it’s why a recipe like these low carb pumpkin cupcakes had to be birthed. 

It’s certainly not the only keto pumpkin recipe you will on the site but these are hearty enough to have for breakfast. In fact, they could have easily been called keto pumpkin muffins because they are a cross between my low carb pumpkin bread and my keto cream cheese pumpkin cake.

You should know that I have a complete list of Keto Cakes that as a fan of cakes I encourage you to also visit.

Keto Pumpkin Cream Cheese Cupcakes 

Keto pumpkin cream cheese cupcakes
Keto Pumpkin Cream Cheese Cupcakes

When I started out to create this recipe I knew one thing was certain, and that’s that, I wanted the pumpkin and spices flavor to be pronounced. It’s why you’ll see that I was generous when it came time to add spices. You can, of course, feel free to reduce the spices by half if that suits you better. 

I’ve topped these low carb pumpkin cupcakes with both a cream cheese frosting or simply a little whipped heavy cream, you know like the one that comes in a can.

However, like I already mentioned these cupcakes are packed with good for you ingredients which is why I skip the frosting and have them for breakfast from time to time.

Why? Well because these keto-friendly pumpkin cupcakes are made golden flax meal. Adding flax meal to these pumpkin muffins gives you a little extra fiber in your diet, something I think we can all have more of, especially while doing a keto diet.

You should know that you can also substitute the flax meal for almond flour in equal amounts if you’re not a fan of flax meal. So you have a few options here. 

The batter of these keto cupcakes is thick and not what you would necessarily expect in cupcakes but I assure you they are worth trying. One cupcake is all you need to quench your pumpkin craving.

Low Carb Keto Pumpkin Recipes

Since I am such a fan of pumpkin recipes I’ve also made a number of low carb keto-friendly recipes that feature this seasonal treat. So do check the following recipes too. I’m sure you are sure to find something you’ll love.

I sure hope you will give this recipe a try. Once you do, make sure you remember to tag us on Instagram and Facebook. It’s what keeps this girl encouraged to keep sharing and perfecting her recipes.

Also, check out our Amazon Store for recommendations. You might be surprised by how many great keto options are at your disposal.

Favorite Keto Hack To Stay On Track

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.

But even when I am at my best I could use a little willpower to stay focused, after all, I’ve come too far to let a food temptation win.

Perhaps, you’ve struggled to get into ketosis consistently on your low carb keto diet, or you’ve hit a plateau that doesn’t seem to budge, consider using Perfect KETO exogenous ketones.

I’m a big fan of exogenous ketones frankly because I have seen how much it helps people stay compliant. By using exogenous ketones you will naturally elevate your ketones allowing you to enter into ketosis more quickly.

Being at a deeper level of ketosis will help reduce your appetite, carb cravings, and give you lasting energy.  It’s been our experience that the use of exogenous ketones helps make the low carb keto lifestyle a viable sustainable option.

Honestly, it’s like having willpower in a cup.  Learn more about the science behind both exogenous and endogenous ketones and have your questions answered from a doctor’s perspective.

Make sure you also pick up your free and complete guide to understanding ketosis. Then begin the ketosis diet easily with this Start-up Guide to the Ketosis Diet.

Wondering which foods you should avoid when doing Keto? This Keto Food Guide will assist you in doing the Keto Diet correctly.

Use this link and get a 15% off discount when you place your order for any of Perfect Keto’s products. Then add the code FITTOSERVE at checkout.

Keto Pumpkin Cream Cheese Cupcakes

Keto Pumpkin Cream Cheese Cupcakes

Yield: 24
Prep Time: 10 minutes
Cook Time: 30 minutes
Total Time: 40 minutes

It's a recipe for keto pumpkin cream cheese cupcakes. These pumpkin cupcakes are low in carbs, sugar-free, gluten-free, grain-free keto-friendly option.


Pumpkin cupcake batter

Cream Cheese Frosting (optional)


Keto Cream Cheese Frosting

  1. Beat the cream cheese and butter until light and fluffy using an electric mixer.
  2. To this add gently add the confectioners sugar-substitute.
  3. Next add the heavy whipping cream a couple of tablespoons at a time and beat until fully combined. 
  4. Set aside until cupcakes are fully cooled before frosting.

Keto Pumpkin Cream Cheese Cupcakes

  1. Pre-heat oven to 350 degrees.
  2. Line two 12 muffin tin pans with muffin liners.
  3. In a small bowl measure and set aside the golden flax meal, baking powder, salt, and spices.
  4. Then a large bowl using an electric mixer beat the softened cream cheese until light and fluffy about 2 minutes.
  5. To this mix add the sugar substitute and continue to beat until well incorporated.
  6. Add the 8 eggs one at a time, combining well after each addition.
  7. Next add the pumpkin puree making sure that it's well combined.
  8. At this point add the dry ingredients into the batter and combine until the batter is well incorporated.


You can substitute the 1 1/2 cups of golden flax meal for 1 1/2 cups of almond flour.

The batter for these pumpkin cream cheese cupcakes will be thick.

The nutrition facts are not including the cream cheese frosting. If you add the frosting add another 1.6 net carbs per cupcakes.

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Nutrition Information:
Yield: 24 Serving Size: 1
Amount Per Serving:Calories: 185 Total Fat: 15.5g Saturated Fat: 7.7g Cholesterol: 91mg Sodium: 91mg Carbohydrates: 5g Fiber: 2.4g Sugar: 0.8g Protein: 5.5g


  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. ?
  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?
    • I use swerve or Splenda. Obviously swerve is much healthier but I can't always afford. In our world it's a matter of picking your evils. Rather use Splenda here and there than for hubby and I go back to diabetes. ?
  6. They look delicious!
  7. Going to have to try these
  8. Pumpkins and cream cheese = heaven.
  9. 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.
  10. 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 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.
  11. Sounds delicious! Love pumpkin season!!
  12. ardith ellis
    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! :)
    • Hi thanks for stopping by. I believe you can although personally I would roast the pumpkin to avoid it getting too watery if you just boil in water. Let me know if it works for you. ?
      • oh, yes! i normally slice or cube butternut & roast it into yummy-ness! thank you for your quick reply - i will let you know how they turn out! [NONE of my food "experiments" go to waste in this household! - yay!]
  13. Sounds great, but I like to know how many carbs are in one cake . Thank you Dorle
  14. 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 ?
  15. I'm a little confused. When you mentioned 4 net carbs, were you referring to your pumpkin cream cheese recipe or when you switch the pumpkins puree for the pumpkin squash.
  16. Just made this using almond flour and the batter wasn't thick, is it because you used the golden flax seed. Also can I substitute regular flax seed for the golden and if so does it change the nutritional calculations?
    • Hi Arena, if you left out the golden flax it would have changed the recipe dramatically and would explain why the batter isn't thick. I have a post on keto baking that may shed more light as to how low carb baking ingredients work and how to best bake with them. I only bake with golden flax because regular flax can make the batter too heavy and it takes longer to bake.

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