Keto Pumpkin Cream Cheese Muffins With a Soft Bakery-Style Center
These Keto Pumpkin Cream Cheese Muffins combine a soft, warmly spiced pumpkin muffin with a creamy cheesecake-style center. Almond flour gives them a tender texture, while coconut flour helps absorb moisture from the pumpkin so the muffins hold together without becoming soggy.
They’re perfect for fall breakfasts, brunch, dessert, or meal prep, and they pair especially well with coffee or a keto pumpkin spice latte.
Jump to Recipe Print RecipeDisclosure: This post may contain affiliate links. Glow & Nourish may earn a commission if you purchase through one of these links, at no additional cost to you.
Why You’ll Love These Keto Pumpkin Muffins
- Soft, moist, and warmly spiced
- Filled with a creamy cheesecake-style center
- Made without traditional wheat flour
- Sweetened without regular granulated sugar
- Perfect for breakfast, brunch, or dessert
- Freezer-friendly
- Made with real pumpkin puree
- Approximately 4 net carbohydrates per muffin
Ingredients You’ll Need
Exact measurements are included in the recipe card below.
Blanched almond flour: Use finely ground almond flour rather than coarse almond meal for a softer muffin texture.
Coconut flour: Helps absorb moisture from the pumpkin and gives the muffins more structure. Do not replace it with almond flour using the same measurement.
Pumpkin puree: Use 100% pure pumpkin puree, not pumpkin pie filling.
Keto-friendly sweetener: A monk fruit-allulose blend works well in both the muffin batter and cream cheese filling. Sweetness can vary by brand.
Eggs: Provide structure and help bind the almond-flour batter.
Butter: Adds richness and moisture. Let melted butter cool slightly before combining it with the eggs.
Unsweetened almond milk: Helps create a scoopable batter without adding much sugar.
Pumpkin pie spice, cinnamon, and nutmeg: Create the warm fall flavor.
Cream cheese: Forms the creamy cheesecake-style center. It should be fully softened before mixing.
Pecans: Optional, but they add a buttery crunch to the tops.
Equipment You’ll Need
Useful tools for this recipe include:
- Standard 12-cup muffin pan
- Silicone or parchment muffin liners
- Large mixing bowl
- Medium mixing bowl
- Hand mixer
- Whisk
- Silicone spatula
- Muffin or cookie scoop
- Cooling rack
- Measuring cups and spoons
How to Make Keto Pumpkin Cream Cheese Muffins
1. Bring the Ingredients to Room Temperature
Remove the eggs and cream cheese from the refrigerator about 30 to 45 minutes before baking.
Room-temperature cream cheese blends more smoothly, while room-temperature eggs combine more evenly with melted butter.
2. Prepare the Oven and Muffin Pan
Preheat the oven to 350°F.
Line a standard muffin pan with 12 silicone or parchment liners.
Lightly grease paper liners when necessary.
3. Make the Cream Cheese Filling
Beat the softened cream cheese for approximately one minute, until smooth.
Add the powdered keto sweetener, egg yolk, and vanilla extract.
Beat again until the filling is creamy and evenly blended.
Set it aside while preparing the pumpkin batter.
4. Mix the Dry Ingredients
In a large bowl, whisk together:
- Almond flour
- Coconut flour
- Granulated sweetener
- Baking powder
- Pumpkin pie spice
- Cinnamon
- Nutmeg
- Salt
Break apart any visible lumps so the baking powder and spices are evenly distributed.
5. Mix the Wet Ingredients
In a separate bowl, whisk together the eggs, pumpkin puree, melted butter, almond milk, and vanilla.
The butter should be warm rather than hot so it doesn’t begin cooking the eggs.
6. Finish the Muffin Batter
Pour the wet ingredients into the dry ingredients.
Stir just until a thick batter forms.
Let the batter rest for three to five minutes so the coconut flour can absorb some of the moisture.
7. Fill the Muffin Cups
Add approximately one generous tablespoon of pumpkin batter to the bottom of each muffin cup.
Place about one tablespoon of cream cheese filling in the center.
Divide the remaining pumpkin batter between the cups, covering most of the cream cheese.
A small amount of exposed filling is fine.
8. Add the Optional Pecan Topping
Mix the chopped pecans, keto sweetener, cinnamon, and melted butter.
Sprinkle a small amount over each muffin and gently press it into the batter.
9. Bake
Bake for 22 to 27 minutes.
The muffins are ready when the tops appear set, the outer pumpkin portion springs back lightly, and a toothpick inserted into the pumpkin portion comes out mostly clean.
Avoid testing directly through the cream cheese center because it will remain soft while warm.
10. Cool Completely
Let the muffins cool in the pan for approximately 15 minutes.
Carefully transfer them to a cooling rack.
Allow them to cool completely before serving. The almond-flour crumb and cream cheese center become firmer as they cool.
Tips for Moist Muffins That Aren’t Soggy
Measure the pumpkin carefully. Adding too much puree can make the centers overly wet.
Use pumpkin puree, not pumpkin pie filling. Pumpkin pie filling contains added sugar and other ingredients.
Do not omit the coconut flour. It helps absorb extra moisture.
Let the batter rest. This gives the coconut flour time to thicken the mixture.
Avoid overmixing. Stir only until the ingredients are combined.
Cool completely before eating. Almond-flour muffins are delicate while warm.
Check the pumpkin portion for doneness. The cream cheese center will remain soft.
Easy Variations
Pumpkin Chocolate Chip Muffins
Fold ⅓ cup of sugar-free chocolate chips into the pumpkin batter.
Pumpkin Pecan Muffins
Fold ½ cup of chopped pecans into the batter and add more to the tops.
Pumpkin Walnut Muffins
Replace the pecans with finely chopped walnuts.
Pumpkin Cheesecake Swirl Muffins
Reserve a small amount of the cream cheese filling and add dots to the tops. Swirl lightly with a toothpick before baking.
Pumpkin Spice Latte Muffins
Add one teaspoon of instant espresso powder to the wet ingredients.
Can You Use Fresh Pumpkin Puree?
Yes, but canned puree generally produces more consistent results.
Fresh puree may contain extra moisture, so drain it before measuring. It should be thick and spoonable rather than watery.
Can You Make Them Without the Cream Cheese Filling?
Yes.
Prepare the pumpkin batter as written and divide it evenly between 12 muffin cups.
Without the filling, the muffins may bake more quickly. Begin checking them after approximately 20 minutes.
How to Store Keto Pumpkin Muffins
Because the muffins contain cream cheese, store them in the refrigerator.
Allow them to cool completely, then place them in an airtight container.
Refrigerate for up to five days.
For the best texture, let a refrigerated muffin sit at room temperature for about 10 minutes before serving.
Can You Freeze Pumpkin Cream Cheese Muffins?
Yes.
Place completely cooled muffins in a freezer-safe container and separate layers with parchment paper.
Freeze for up to two months.
Thaw overnight in the refrigerator before serving.
What to Serve With Keto Pumpkin Muffins
Serve them with:
- Hot coffee
- Cold brew
- Keto pumpkin spice latte
- Unsweetened almond milk latte
- Chai tea
- Scrambled eggs
- Bacon
- Turkey sausage
- Greek yogurt
- Fresh berries
- Sugar-free whipped cream
Frequently Asked Questions
Why are my muffins wet in the middle?
The batter may contain too much pumpkin, the coconut flour may have been omitted or undermeasured, or the muffins may need more baking time.
Can I replace almond flour with coconut flour?
No. Coconut flour absorbs much more liquid than almond flour and cannot be substituted in equal amounts.
Can I use a different sweetener?
Yes, but different sweeteners vary in sweetness, texture, browning, and cooling effect. Use a baking sweetener designed to measure similarly to sugar.
Why did the cream cheese sink?
A softer filling may settle slightly during baking. Make sure the cream cheese is softened but not melted, and keep the filling centered inside the batter.
Are these muffins gluten-free?
They can be, but only when all packaged ingredients are confirmed gluten-free.
Find More Fall Keto Recipes
Keto Recipe Vault includes searchable keto breakfasts, dinners, snacks, soups, desserts, drinks, comfort foods, and seasonal recipes, so you can find something that fits your craving without searching through multiple sites.
Keto Pumpkin Cream Cheese Muffins
Ingredients
Equipment
Method
- Remove the eggs and cream cheese from the refrigerator 30 to 45 minutes before baking.
- Preheat the oven to 350°F.
- Line a standard muffin pan with 12 silicone or parchment liners.
- Beat the softened cream cheese for approximately one minute, until smooth.
- Add the powdered sweetener, egg yolk, and vanilla. Beat until creamy, then set aside.
- In a large bowl, whisk together the almond flour, coconut flour, granulated sweetener, baking powder, pumpkin pie spice, cinnamon, nutmeg, and salt.
- In a separate bowl, whisk together the eggs, pumpkin puree, melted butter, almond milk, and vanilla.
- Pour the wet ingredients into the dry ingredients and stir just until combined.
- Let the batter rest for three to five minutes.
- Add approximately one generous tablespoon of pumpkin batter to each muffin cup.
- Place approximately one tablespoon of cream cheese filling in the center of each cup.
- Divide the remaining pumpkin batter between the cups, covering most of the filling.
- If using the topping, combine the pecans, sweetener, cinnamon, and melted butter.
- Sprinkle the pecan mixture over the muffins.
- Bake for 22 to 27 minutes, until the pumpkin portion is set and springs back lightly.
- Let the muffins cool in the pan for approximately 15 minutes.
- Transfer them to a cooling rack and cool completely.
- Refrigerate before storing.
Notes
- Use 100% pumpkin puree, not pumpkin pie filling.
- Measure the coconut flour carefully because it is highly absorbent.
- Do not add extra pumpkin.
- Let the batter rest before filling the muffin cups.
- Avoid inserting the toothpick directly through the cream cheese center.
- The muffins become firmer as they cool.
- Store the finished muffins in the refrigerator.
- Nutrition does not include the optional pecan topping unless specifically calculated.
- Sweetener, almond flour, pumpkin, and cream cheese brands can affect the nutrition.
Estimated Nutrition Per Muffin
Based on 12 muffins without the optional pecan topping:- Calories: approximately 285
- Protein: approximately 7 g
- Fat: approximately 26 g
- Saturated fat: approximately 10 g
- Total carbohydrates: approximately 8 g
- Dietary fiber: approximately 4 g
- Net carbohydrates: approximately 4 g
- Sugar: approximately 2 g
- Sodium: approximately 240 mg
