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Keto Pumpkin Muffins With Cream Cheese
Keto fall baking recipes like these Keto Pumpkin Muffins With Cream Cheese are the ultimate low-carb treats for autumn. Made with almond flour, warm pumpkin spices, and a velvety cream cheese filling, these muffins are ready in under 40 minutes and yield 8 perfectly portioned servings. Perfect as a snack, dessert, or even a breakfast on the go, they are tender, flavorful, and satisfyingly sweet without the sugar.
As someone who often bakes for my son Theo, I love recipes like these that are indulgent yet keto-friendly. They’ve quickly become a family favorite, especially during cooler months when pumpkin cravings hit hard.
Table of Contents
- Why are these muffins special?
- What ingredients do you need for Keto Pumpkin Muffins With Cream Cheese?
- How do you make Keto Pumpkin Muffins With Cream Cheese step by step?
- Frequently Asked Questions About Keto Pumpkin Muffins With Cream Cheese
- Expert Tips for Perfect Keto Pumpkin Muffins
- What are some easy ingredient swaps for this recipe?
- How to store and reheat Keto Pumpkin Muffins With Cream Cheese
Why are these muffins special?
Keto Pumpkin Muffins With Cream Cheese are special because they combine the rich, warm flavors of pumpkin spice with a creamy, luscious filling—all while being low-carb and keto-friendly. They’re perfect for fall baking and feel indulgent without the guilt.
- Low-Carb Indulgence: These muffins are made with almond and coconut flour, making them perfect for anyone following a keto lifestyle.
- Rich in Flavor: Warm spices like cinnamon, nutmeg, and ginger create the ultimate fall flavor in every bite.
- Creamy Center: A sweetened cream cheese filling perfectly complements the spiced pumpkin batter.
- Quick and Easy: Ready in under 40 minutes, this recipe is as convenient as it is satisfying.
What ingredients do you need for Keto Pumpkin Muffins With Cream Cheese?
This recipe calls for a mix of keto-friendly flours, sweeteners, and spices to create a perfectly textured muffin with a sweet, creamy filling. Here’s everything you’ll need:
- 1 cup almond flour
- 1/4 cup coconut flour
- 1/4 cup granulated erythritol or other keto-friendly sweetener
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1 teaspoon ground cinnamon
- 1/2 teaspoon ground nutmeg
- 1/4 teaspoon ground ginger
- 1/4 teaspoon ground cloves
- 1/4 teaspoon salt
- 2 large eggs
- 1/2 cup canned pumpkin puree (unsweetened)
- 1/4 cup unsweetened almond milk
- 1/4 cup melted unsalted butter or coconut oil
- 1 teaspoon vanilla extract
- 4 ounces cream cheese, softened
- 2 tablespoons powdered erythritol (for cream cheese filling)
- 1/2 teaspoon vanilla extract (for cream cheese filling)
The almond flour provides a light, tender crumb, while the pumpkin puree infuses natural moisture and earthy depth. The erythritol keeps it sweet without added sugars, making it keto-compliant.
How do you make Keto Pumpkin Muffins With Cream Cheese step by step?
Making these Keto Pumpkin Muffins With Cream Cheese is straightforward, with just a few steps to mix, fill, and bake your way to perfection. Here’s how it’s done:
Step 1 — Preheat the Oven
Preheat your oven to 350°F (175°C) and prepare a muffin tin by lining it with 8 paper liners or lightly greasing it with cooking spray.
You might also enjoy our starbucks pumpkin cream cheese muffins.
Step 2 — Combine the Dry Ingredients
In a medium mixing bowl, whisk together the almond flour, coconut flour, granulated erythritol, baking powder, baking soda, cinnamon, nutmeg, ginger, cloves, and salt.
Step 3 — Mix the Wet Ingredients
In a separate large bowl, whisk the eggs, pumpkin puree, almond milk, melted butter, and vanilla extract until smooth and well combined.
Step 4 — Combine Batter
Gradually stir the dry ingredients into the wet ingredients, mixing until a thick, cohesive batter forms.

Step 5 — Prepare Cream Cheese Filling
In a small bowl, beat the softened cream cheese, powdered erythritol, and vanilla extract until smooth and creamy.
For more ideas, check out our moist pumpkin cream cheese muffins.
Step 6 — Assemble the Muffins
Spoon about 2 tablespoons of batter into each muffin cup. Add 1 teaspoon of cream cheese filling to the center, then top with another tablespoon of batter, fully enclosing the filling.
Step 7 — Bake and Cool
Bake in the preheated oven for 20–25 minutes, or until a toothpick inserted into the muffin (avoiding the cream cheese center) comes out clean. Let the muffins cool for 5 minutes before transferring to a wire rack to cool completely.
Frequently Asked Questions About Keto Pumpkin Muffins With Cream Cheese
Can I use other sweeteners?
Yes, any keto-friendly granulated sweetener like monk fruit or allulose can work in place of erythritol. Adjust sweetness to taste.
Can I make this dairy-free?
Yes, replace cream cheese with a dairy-free alternative and butter with coconut oil for a dairy-free version.
Looking for something similar? Try our healthy pumpkin cream cheese muffins.
How do I avoid overbaking?
Check the muffins at the 20-minute mark and look for a clean toothpick (excluding the cream cheese center). Overbaking can dry them out.
How long can these muffins be stored?
These muffins can be refrigerated in an airtight container for up to 5 days or frozen for up to 3 months.
Why is the batter so thick?
The combination of almond and coconut flours naturally creates a thicker batter. This texture helps hold the cream cheese filling in place.
Expert Tips for Perfect Keto Pumpkin Muffins
- Room Temperature Ingredients: Ensure eggs and cream cheese are at room temperature for easier mixing and better texture.
- Don’t Skimp on Spices: The blend of cinnamon, nutmeg, ginger, and cloves brings out the best pumpkin flavor.
- Use a Cookie Scoop: For even portioning of batter and filling, a cookie scoop is a handy tool.
- Cool Completely: Allow muffins to cool fully before serving to let the flavors and textures settle.
What are some easy ingredient swaps for this recipe?
You can tailor this recipe to suit dietary preferences or available pantry items with a few swaps:
- Butter: Substitute coconut oil for a dairy-free option with a subtle tropical note.
- Almond Milk: Swap in any unsweetened plant-based milk like cashew or hemp milk.
- Cream Cheese: Use coconut cream or a vegan cream cheese alternative for a dairy-free filling.
How to store and reheat Keto Pumpkin Muffins With Cream Cheese
To keep your muffins fresh, store them in an airtight container in the fridge for up to 5 days. For longer storage, freeze in a sealed bag for up to 3 months. Thaw overnight in the fridge.
To reheat, microwave a muffin for 15–20 seconds to warm it up without drying it out. Alternatively, you can use a low oven (300°F) for 5 minutes for a freshly baked feel.
Keto Pumpkin Muffins With Cream Cheese
Equipment
- Mixing bowl
- Whisk
- muffin tin
- Oven
- Wire rack
Ingredients
- 1 cup almond flour
- 1/4 cup coconut flour
- 1/4 cup granulated erythritol (or other keto-friendly sweetener)
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1 tsp ground cinnamon
- 1/2 tsp ground nutmeg
- 1/4 tsp ground ginger
- 1/4 tsp ground cloves
- 1/4 tsp salt
- 2 large eggs
- 1/2 cup canned pumpkin puree (unsweetened)
- 1/4 cup unsweetened almond milk
- 1/4 cup melted unsalted butter (or coconut oil)
- 1 tsp vanilla extract
- 4 oz cream cheese (softened)
- 2 tbsp powdered erythritol (for cream cheese filling)
- 1/2 tsp vanilla extract (for cream cheese filling)
Instructions
- Preheat your oven to 350°F (175°C) and line a muffin tin with 8 paper liners or lightly grease it with cooking spray.
- In a medium mixing bowl, whisk together almond flour, coconut flour, granulated erythritol, baking powder, baking soda, cinnamon, nutmeg, ginger, cloves, and salt.
- In a separate large bowl, whisk together the eggs, pumpkin puree, almond milk, melted butter, and vanilla extract until smooth and well combined.
- Slowly add the dry ingredients to the wet ingredients, stirring until a thick batter forms.
- In a small bowl, beat the softened cream cheese, powdered erythritol, and vanilla extract for the filling until smooth and creamy.
- Spoon about 2 tablespoons of the muffin batter into each prepared muffin cup. Add about 1 teaspoon of the cream cheese filling to the center of each, then cover with another 1 tablespoon of batter, ensuring the cream cheese is fully enclosed.
- Bake in the preheated oven for 20–25 minutes, or until the muffins are golden brown and a toothpick inserted into the muffin (not the cream cheese center) comes out clean.
- Allow the muffins to cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely before serving.
Notes

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