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Low carb pumpkin muffins easy is a delightful fall-inspired treat made with almond flour, coconut flour, unsweetened pumpkin puree, and warm spices. This gluten-free and keto-friendly recipe is ready in just 40 minutes and yields 12 muffins. The cream cheese swirl adds a luscious touch of sweetness and a creamy texture to each bite.
I first discovered the joy of swirling cream cheese into pumpkin batter one autumn afternoon when baking for my son Theo. The way the flavors combined created a perfect balance of sweet and spiced warmth, and these muffins instantly became a family favorite.
Table of Contents
- Why is Low Carb Pumpkin Muffins With Cream Cheese Swirl so special?
- What ingredients do you need for Low Carb Pumpkin Muffins With Cream Cheese Swirl?
- How do you make Low Carb Pumpkin Muffins With Cream Cheese Swirl step by step?
- Frequently Asked Questions About Low Carb Pumpkin Muffins With Cream Cheese Swirl
Why is Low Carb Pumpkin Muffins With Cream Cheese Swirl so special?
Low Carb Pumpkin Muffins With Cream Cheese Swirl combine the rich, earthy flavors of pumpkin with the creamy sweetness of cream cheese for a keto-friendly fall treat. The swirl design creates a visually stunning dessert that’s equally delicious.
- The almond and coconut flour base ensure these muffins are gluten-free and low-carb without sacrificing texture.
- Pumpkin puree adds both moisture and depth of flavor, highlighting the seasonal spices.
- The cream cheese filling elevates each bite with a smooth, tangy sweetness that balances the spices beautifully.
What ingredients do you need for Low Carb Pumpkin Muffins With Cream Cheese Swirl?
This recipe uses wholesome low-carb ingredients to achieve incredible flavor and texture while remaining gluten-free and keto-friendly.
- 1 cup almond flour
- 1/4 cup coconut flour
- 1/4 cup granulated erythritol or your preferred low-carb sweetener
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1 tsp ground cinnamon
- 1/2 tsp ground nutmeg
- 1/4 tsp ground cloves
- 1/4 tsp salt
- 3/4 cup unsweetened pumpkin puree
- 2 large eggs
- 1/4 cup unsweetened almond milk
- 1/4 cup melted coconut oil
- 1 tsp vanilla extract
- 4 oz cream cheese, softened
- 2 tbsp powdered erythritol (for cream cheese filling)
- 1/4 tsp vanilla extract (for cream cheese filling)
Almond flour provides a tender crumb, while coconut flour adds structure and absorbs moisture, creating the perfect base for these muffins.
How do you make Low Carb Pumpkin Muffins With Cream Cheese Swirl step by step?
This recipe involves simple steps to create moist pumpkin muffins with a luxurious cream cheese swirl. Follow these instructions for best results.
Step 1 — Preheat the oven and prepare the pan
Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease with non-stick spray.
You might also enjoy our pumpkin cream cheese swirl muffins.
Step 2 — Mix the dry ingredients
In a large mixing bowl, whisk together almond flour, coconut flour, granulated erythritol, baking powder, baking soda, cinnamon, nutmeg, cloves, and salt.
Step 3 — Combine the wet ingredients
In a separate bowl, mix pumpkin puree, eggs, almond milk, melted coconut oil, and vanilla extract until smooth and combined.
Step 4 — Blend wet and dry ingredients
Gradually add the wet ingredients to the dry ingredients, stirring until fully incorporated and no lumps remain.

Step 5 — Make the cream cheese filling
In a small bowl, mix softened cream cheese, powdered erythritol, and vanilla extract until smooth.
For more ideas, check out our how to make pumpkin cream.
Step 6 — Fill and swirl the batter
Fill each muffin cup about 2/3 full with the pumpkin batter. Spoon a small dollop of cream cheese filling onto the center of each muffin and use a toothpick or knife to gently swirl it into the batter.
Step 7 — Bake the muffins
Bake for 20-25 minutes, or until a toothpick inserted into the muffin (avoiding the cream cheese swirl) comes out clean. Allow the muffins to cool in the pan for 5-10 minutes before transferring to a wire rack to cool completely.
Frequently Asked Questions About Low Carb Pumpkin Muffins With Cream Cheese Swirl
Can I use regular sugar instead of erythritol?
Yes, you can substitute regular sugar for erythritol, but the recipe will no longer be keto or low-carb.
How do I ensure the cream cheese swirl stays visible?
Swirl the cream cheese lightly and avoid over-mixing it into the batter to maintain a defined pattern.
Looking for something similar? Try our starbucks pumpkin cream cheese muffins.
Why did my muffins sink in the middle?
Muffins may sink if the batter is overmixed or if too much cream cheese filling is used in the center.
How should I store these muffins?
Store the muffins in an airtight container in the refrigerator for up to 5 days. You can also freeze them for up to 3 months.
Can I make this recipe dairy-free?
To make it dairy-free, replace the cream cheese with a plant-based alternative and use almond milk instead of any dairy milk.
Low Carb Pumpkin Muffins With Cream Cheese Swirl
Equipment
- Mixing bowl
- Whisk
- muffin tin
- Oven
- Toothpick
Ingredients
- 1 cup almond flour
- 1/4 cup coconut flour
- 1/4 cup granulated erythritol (or your preferred low-carb sweetener)
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1 tsp ground cinnamon
- 1/2 tsp ground nutmeg
- 1/4 tsp ground cloves
- 1/4 tsp salt
- 3/4 cup unsweetened pumpkin puree
- 2 large eggs
- 1/4 cup unsweetened almond milk
- 1/4 cup melted coconut oil
- 1 tsp vanilla extract
- 4 oz cream cheese (softened)
- 2 tbsp powdered erythritol (for cream cheese filling)
- 1/4 tsp vanilla extract (for cream cheese filling)
Instructions
- Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners or grease with non-stick spray.
- In a large mixing bowl, whisk together almond flour, coconut flour, granulated erythritol, baking powder, baking soda, cinnamon, nutmeg, cloves, and salt.
- In a separate bowl, combine pumpkin puree, eggs, almond milk, melted coconut oil, and vanilla extract. Whisk until smooth.
- Gradually add the wet ingredients to the dry ingredients, stirring until fully incorporated and no lumps remain.
- In a small bowl, make the cream cheese filling by mixing softened cream cheese, powdered erythritol, and vanilla extract until smooth.
- Fill each muffin cup about 2/3 full with the pumpkin batter.
- Spoon a small dollop of the cream cheese filling onto the center of each muffin and use a toothpick or knife to gently swirl it into the batter.
- Bake for 20-25 minutes, or until a toothpick inserted into the muffin (avoiding the cream cheese swirl) comes out clean.
- Allow the muffins to cool in the pan for 5-10 minutes before transferring to a wire rack to cool completely.
Notes

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