These keto pumpkin cheesecake muffins with coconut flour are moist and incredibly easy to make. The sweet cream cheese swirl takes this gluten free keto dessert to the next level! Deliciously flavoured with pumpkin spice and only 2.9 grams of net carbs per muffin.
My whole family loves these Keto Pumpkin Muffins with Coconut Flour. They are great as a grab and go snack and also like them with a dollop of sour cream as a sweet snack or even for breakfast.
That’s why I decided to take the recipe a step further to make these keto pumpkin cheesecake muffins!
Basically, it is the same low carb gluten free recipe, only with an added cream cheese swirl at the top. The result is, if I may say so, just SO GOOD – definitely on a par with my Low Carb Sugar Free Banana Bread. Trust me, you may want to go for seconds.
Keto pumpkin muffins will never be as light and airy as regular pumpkin muffins made with wheat and sugar. That’s just the nature of coconut flour. They are moist and satisfying – a delicious way to enjoy this autumn staple without piling on the carbs!
Before I get to the recipe, let me answer a question I get asked a lot:
Is pumpkin Keto?
Absolutely! Pumpkin, or winter squash, is relatively low in carbs and in moderation perfect for a keto diet. Cooked puree from regular pumpkin (giant pumpkin / Halloween pumpkin) contains around 5 grams of net carbs per 100 grams.
Note that butternut squash is much higher in carbs at 12 grams per 100 grams!
How to make keto pumpkin cheesecake muffins
Here are all the ingredients we need. I actually ended up using twice as much cream cheese as shown in the image because I felt the muffins needed a bit more cheesecake topping.
Tip: I used pumpkin puree from a can, but you can also make your own. Recipe for homemade pumpkin puree is further down in the post!
1.) In a food processor or in a bowl with a hand-held electric blender, mix the pumpkin puree and eggs until frothy.
2.) Add the all other ingredients except the walnuts (if you’re using them) and blend until smooth.
3.) Last, fold in the walnuts. I like the crunch they add and the flavour works well with the pumpkin. However, they are not essential for the recipe. If you prefer a nut free muffin, just leave them out.
Let the batter sit for a couple of minutes so the coconut flour can absorb the moisture. As you can see, that batter is fairly thick and needs to be spooned rather than poured.
4.) Then scoop the mix into a muffin pan lined with paper cups. Under no circumstances, omit the paper cups because your muffins will stick. An alternative would be using silicone cups.
Next, mix the cheesecake filling in a small bowl using a spoon (no image for this, sorry!).
Dollop the mix on top of the batter and swirl a little with a skewer or toothpick. Option to press a little deep into the middle of the batter too if you prefer some in the centre of the muffin. Top with a sprinkling of reserved chopped nuts.
Bake around 25 minutes or until lightly browned on top and you can insert and remove a skewer without it being sticky. All ovens are different!
Tip: If your muffins aren’t done yet but the cheesecake topping is browned enough, loosely place aluminium paper over the tops.
What is pumpkin puree
When you buy pumpkin puree, do not mistake it for pumpkin pie filling. Pumpkin pie filling contains spices and tons of sugar.
Look out for 100% pure pumpkin. Basically, it’s cooked and mashed pumpkin and nothing else.
Recipe for homemade pumpkin puree
Pumpkin puree is readily available in the US. In the UK, you can get it all year round at supermarkets such as Waitrose and Tesco. This is a recent thing, so – yay.
However, in some countries, canned pumpkin is still hard to find. In this case, just make your own pumpkin puree. Here is how:
- Preheat the oven to 200 C / 400 F.
- Cut a pumpkin in half and scoop out the seeds. Then, place the halves flesh-side down on a tray lined with parchment paper.
- Roast for 30-45 minutes, depending on the size of the pumpkin.
- Let the pumpkin cool, then scoop out the flesh and discard the skins.
- Blend into a puree.
Recipe for homemade pumpkin spice mix
I normally use what we in the UK call “mixed spice” in place of pumpkin spice mix.
If you can’t get either, just make your own pumpkin spice mix. The absolutely essential ingredients are cinnamon, nutmeg and ginger – don’t worry if you don’t have all the others.
ground allspice (1 Tbs )
cinnamon (1 Tbs)
mace (2 tsp)
nutmeg (1 Tbs)
cloves (1 tsp)
coriander (1 tsp)
ginger (1 tsp)
Mix and store the leftovers for future use in pumpkin recipes and Christmas cookies.
I always like to give my readers options to substitute ingredients. Here are the most common subs:
Low carb pumpkin muffins with almond flour
If you prefer baking with almond flour, use 1 1 /2 cups instead of the coconut flour.
Nut free muffins
As mentioned above, the walnuts in the recipe are optional and can be left out. In place of the coconut, you can also use seed flours. I recommend 1 cup sunflower seed flour mixed with 1/2 cup sesame seed flour.
Note: I grind these myself in a high speed blender, which is cheaper than buying them ready-made.
Dairy free keto pumpkin muffins
I have not yet tried this myself, but I would recommend following substitutions:
Swap out the butter for coconut oil when making the muffin batter.
For the filling, use use coconut cream instead of dairy cream. There are dairy free cream cheeses by Daiya and Kite Hill which US based readers have recommended.
You can also look into homemade dairy free cream cheese. Recipes normally use either cashews (higher in carbs) or coconut. Here is a nut free recipe.
How to store keto pumpkin cheesecake muffins
Store your pumpkin muffins in an airtight container in the fridge for up for 5 days. This recipe is freezer-friendly! Freeze in ziplock bags for up to 3 months and defrost on the counter or in the fridge.
More Keto pumpkin desserts:
Tried this recipe? Give it a star rating below!
Keto Pumpkin Cheesecake Muffins
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- 3/4 cup/ 180g pumpkin puree (if using cups, measure generously)
- 4 eggs large
- 1/2 cup plus 1 tbsp / 75g coconut flour
- 1/3 cup / 80g butter unsalted melted
- 1/4 cup / 50g granulated sweetener (So Nourished)
- 1 tsp baking powder
- 1 tsp pumpkin spice
- 1 tsp cinnamon
- 1 tsp vanilla
- 1/3 cup / 40g chopped walnuts optional
- Preheat the oven to 175 Celsius / 350 Fahrenheit.
- In a food processor or in a bowl with a hand-held electric blender, mix your pumpkin and eggs until smooth.
- Add the all other ingredients except the walnuts (if using) and blend until smooth.
- Last, add the nuts if using, keeping about 2 tbsp aside for the top, and blend briefly. The nuts are not essential for the recipe and you can leave them out, but their flavours work really well with the pumpkin.
- Let the batter sit for a couple of minutes so the coconut flour can absorb the moisture.
- Then scoop into a muffin pan lined with paper cups.
- Mix the filling (cream cheese, cream, vanilla extract and powdered sweetener) in a small bowl using a spoon. Dollop on top of the batter and swirl a little with a skewer or toothpick. Option to press a little deep into the middle of the batter too if you prefer some in the middle. Top with a sprinkling of reserved chopped nuts.
- Bake around 25 minutes or until lightly browned on top and you can insert and remove a skewer without it being sticky.
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