These muffins have a permanent spot on my fall baking roster, right alongside Pumpkin Cranberry Bread and Strawberry Cream Cheese Muffins.
Pull Cream Cheese Pumpkin Muffins out of the oven and the whole kitchen smells like pumpkin spice — warm, buttery, and sweet in a way that feels right for the season. The real standout here is the filling: a sweetened cream cheese mixture that you spoon right on top of the pumpkin batter and swirl through with a toothpick before baking. It bakes into a ribbon through the center of each muffin that stays creamy and rich against the spiced pumpkin crumb.
The base is made with coconut flour instead of almond flour, and I want to be upfront about that: coconut flour is notorious for making baked goods dry. The pumpkin puree and the cream cheese swirl are doing real work here, keeping the crumb soft and moist rather than chalky. The process is also straightforward — you melt the butter and coconut oil together first, then mix the wet ingredients, add the dry, and mix the filling separately. Even if you don’t bake often, this one is a good starting point.
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Reader Love
These were soooo DELICIOUS!! I usually do not like baked goods with coconut flour because of the dry texture but these were not dry or chalky at all!! They were super moist and buttery. Perfect for fall! Thanks for the pumpkin fix.
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💛 Why you’ll love this recipe
- Moist crumb, not dry: Coconut flour can make baked goods dry, but the pumpkin puree and cream cheese swirl keep every muffin soft and moist all the way through.
- Cream cheese swirl through the center: A sweetened filling — cream cheese, heavy cream, powdered monk fruit sweetener, and vanilla — gets spooned on top and swirled in with a toothpick before baking.
- Simple process: Two bowls, an electric mixer, a toothpick for the swirl, and one muffin tin. No special equipment beyond that.
- Made without almond flour: If almond flour isn’t your thing or you’re out of it, coconut flour does the job here.
- A natural fall recipe: Pumpkin puree and pumpkin pie spice in every bite, great for breakfast, brunch, or a fall gathering.
- Makes 12: The recipe yields a full dozen, so there’s enough to share or have on hand through the week.
⏲ How to make this recipe
Preheat oven to 350 degrees and line muffin tin with muffin liners. Melt together butter and coconut oil.
Muffin Batter: To a mixing bowl, add eggs, egg white, golden monk fruit sweetener, pumpkin puree, melted butter, melted coconut oil, pumpkin pie spice, and vanilla extract and mix together using an electric mixer.
Then, add coconut flour, cream of tartar, baking soda, and salt, and mix again with an electric mixer.
Spoon mixture into muffin liners.
Filling: In a separate bowl, combine filling ingredients and mix with a spoon until well-combined.
Spoon filling mixture into muffin liners atop pumpkin mixture. Using a toothpick, swirl filling into pumpkin mixture.
Final Steps: Bake muffins until toothpick can be poked into center and come out cleanly, about 30-35 minutes.
Remove muffin tin from oven and allow muffins to almost fully cool at room temperature before serving.
👉 Easy ingredient swaps
- Unsalted butter → coconut oil: Swap them 1:1 in either direction. Use all butter, all coconut oil, or the combination the recipe calls for.
- Pumpkin pie spice: Make your own at home with spices from your pantry, or use storebought — it’ll be in the spice aisle. Either works here.
- Golden monk fruit sweetener → Classic monk fruit sweetener, Swerve, Truvia, or erythritol all work at a 1:1 ratio. A few readers have also used coconut sugar or brown sugar with good results, though the bake time may need to run a bit longer.
- Golden monk fruit sweetener → Powdered monk fruit sweetener: The swap works, but the weight differs. For the 1 cup (192g) of golden monk fruit the recipe calls for, use 1 cup (120g) of powdered monk fruit sweetener instead.
- Powdered monk fruit sweetener (in the filling) → granular sweetener: Pulse it in a food processor until powdered before using in the filling.
- Heavy whipping cream (in the filling) → dairy-free option: Sara hasn’t tested this, but canned coconut milk may work alongside a dairy-free cream cheese for the filling. If you try it, leave a comment with how it goes.
✨ Variations
- Double the cream cheese filling: At least one reader doubled the filling and used the extra egg yolk instead of the heavy cream to bring it together — and loved the result. If you’re a cream cheese fan, it’s worth trying.
- Reduce the sweetener: Several readers found the full amount of golden monk fruit sweetener very sweet, with a noticeable cooling aftertaste from the erythritol. Sara confirms you can cut back on the amount to your preference.
- Add almond flour to reduce crumbliness: One reader added ¾ cup of superfine almond flour and found it helped with texture. This changes the flour balance, so results will vary from the original recipe.
- Skip the swirl: If the toothpick swirl doesn’t work out, just spoon the cream cheese filling on top of the batter and leave it there. It bakes up fine either way — several readers have done exactly this.
〰️ How to serve
- Serve warm — allow the muffins to cool at room temperature until nearly cool before serving. If you’re pulling a muffin from the refrigerator, reheat it in the oven at 350°F or in the microwave for about 20 seconds; this softens everything back up and makes it easier to peel away the muffin liner.
- These work well for a fall breakfast or brunch spread alongside coffee or tea.
- They also travel well to parties or fall gatherings — pack them in an airtight container and they hold up well.
- For more fall baking, the Flourless Pumpkin Spice Pancakes bring a similar pumpkin-spice heat, or try the Applesauce Coffee Cake for a soft, spiced bake in a different form.
💬 FAQs
Can I bake these in a 9×13 pan instead of a muffin tin?
Sara recommends sticking with a standard muffin tin for this recipe. Baking the batter in a 9×13 pan would change the thickness and baking time significantly, and the recipe hasn’t been tested that way — results could be unreliable.
How do I store these muffins after baking?
Refrigerator: Once the muffins have cooled, store them in an airtight container in the refrigerator. Reheat in the oven at 350°F or in the microwave for about 20 seconds before eating — this softens them back up and makes it easier to peel the liner away. Freezer: Store cooled muffins in an airtight freezer bag. When you’re ready to eat one, thaw in the refrigerator, then reheat in the oven at 350°F until warmed through.
Where can I buy monk fruit sweetener, and what can I substitute?
Lakanto makes both the golden and powdered monk fruit sweetener this recipe calls for — you can order directly from their website or find it at specialty grocery stores and Costco. If you can’t find monk fruit sweetener, Swerve or Truvia substitute at a 1:1 ratio. Classic monk fruit sweetener and erythritol also work at 1:1.
Why does coconut flour sometimes make baked goods dry, and how does this recipe avoid that?
Coconut flour absorbs far more liquid than almond flour, which is what makes so many coconut flour baked goods turn out dry when the recipe isn’t specifically built around it. Here, the pumpkin puree and the cream cheese swirl both add moisture, so the muffins come out soft rather than chalky.
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Cream Cheese Pumpkin Muffins
Ingredients
Muffins:
- 4 eggs
- 1 egg white
- 1 cup 192g golden monk fruit sweetener
- 1 cup 244g pumpkin puree
- ½ cup 4 oz unsalted butter, melted
- 2 tablespoons 28g coconut oil, melted
- 1 tablespoon pumpkin pie spice
- 2 teaspoons pure vanilla extract
- ½ cup + 2 tbsp, 70g coconut flour
- 2 teaspoons cream of tartar
- 1 teaspoon baking soda
- ¼ teaspoon salt
Filling:
- 3 ounces cream cheese, softened
- 1 tablespoon 15 mL heavy whipping cream
- 1 tablespoon 7g powdered monk fruit sweetener
- ½ teaspoon pure vanilla extract
Instructions
- Preheat oven to 350 degrees and line muffin tin with muffin liners.
- Muffin Batter: To a mixing bowl, add eggs, egg white, golden monk fruit sweetener, pumpkin puree, melted butter, melted coconut oil, pumpkin pie spice, and vanilla extract and mix together using an electric mixer. Then, add coconut flour, cream of tartar, baking soda, and salt, and mix again with an electric mixer. Spoon mixture into muffin liners.
- Filling: In a separate bowl, combine filling ingredients and mix with a spoon until well-combined. Spoon the filling mixture atop pumpkin batter in the muffin liners. Using a toothpick, swirl filling into pumpkin mixture.
- Final Steps: Bake muffins until the toothpick can be poked into the center and come out cleanly about 30-35 minutes.
- Remove muffin tin from oven and allow muffins to almost fully cool at room temperature before serving.
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