Keto Pumpkin Cheesecake Muffins

These keto pumpkin cheesecake muffins are soft, moist, and packed with cozy pumpkin spice flavor, with a creamy cheesecake swirl tucked into every bite. They’re basically pumpkin muffins and cheesecake combined into one seriously good fall treat.

I love these when pumpkin season starts because they feel a little more special than regular pumpkin muffins without being complicated. The cheesecake center stays creamy while the pumpkin muffin around it is tender and perfectly spiced.

They’re great for a fall breakfast with coffee, an afternoon treat, or something sweet to make for Thanksgiving. And if you love pumpkin and cream cheese together, these are definitely worth adding to your fall baking list.

Is Pumpkin Keto-Friendly?

Yes, pumpkin can fit into a keto or low-carb diet when used in moderate portions. It contains some natural carbohydrates, but a little goes a long way when you’re baking with it.

This recipe uses 3/4 cup pumpkin puree for 12 muffins, giving you plenty of pumpkin flavor without using a large amount in each serving.

Make sure you use plain pumpkin puree, not pumpkin pie filling. Pumpkin pie filling usually contains added sugar and spices.

Have extra pumpkin puree to use up? It also works beautifully in this creamy keto pumpkin soup.

Why You’ll Love These Keto Pumpkin Cheesecake Muffins

• Soft, moist pumpkin muffins with a creamy cheesecake center.
• Warmly flavored with pumpkin pie spice and vanilla.
• About 10 minutes of prep and 20 minutes of baking.
• Makes 12 muffins, so they’re great for sharing or meal prep.
• Easy to prepare ahead for Thanksgiving, Halloween, or fall brunches.
• Gluten-free, sugar-free, and low carb when made with the ingredients listed.

Keto Pumpkin Cheesecake Muffins Ingredients

The ingredients are simple and easy to find. Here’s what you’ll need for the pumpkin muffin batter and creamy cheesecake filling.

For the Pumpkin Muffin Batter

• Eggs – Give the muffins structure and help bind the batter together.
• Almond Flour – Creates a soft, tender texture while keeping the muffins gluten-free and low carb.
• Coconut Flour – Works with the almond flour to absorb extra moisture from the pumpkin.
• Pumpkin Puree – Use plain canned or homemade pumpkin puree, not pumpkin pie filling.
• Pumpkin Pie Spice – Gives the muffins their warm fall flavor. You can use store-bought or make your own pumpkin pie spice.
• Heavy Whipping Cream – Adds moisture and richness to the pumpkin batter.
• Sweetener – Use your preferred keto-friendly sweetener that measures like sugar.
• Butter – Melt the butter and allow it to cool slightly before adding it to the eggs.
• Vanilla Extract – Adds sweetness and rounds out the pumpkin spice flavor.
• Baking Powder – Helps the muffins rise and gives them a lighter texture.

For the Cheesecake Filling

• Cream Cheese – Use softened cream cheese so the filling mixes smoothly.
• Egg – Helps set the cheesecake filling as it bakes.
• Sweetener – Sweetens the cream cheese layer without added sugar.
• Almond Flour – Helps thicken and stabilize the cheesecake filling.
• Vanilla Extract – Adds extra flavor to the creamy filling.

How to Make Keto Pumpkin Cheesecake Muffins

These pumpkin muffins with cream cheese filling are easy to put together, and both the batter and cheesecake mixture come together in just a few minutes.

1. Preheat the oven. Preheat your oven to 350°F (180°C) and line a 12-cup muffin pan with paper or silicone liners.
2. Start the pumpkin muffin batter. Add the 5 eggs, melted and slightly cooled butter, and 3/4 cup sweetener to a large mixing bowl. Whisk until smooth and well combined.
3. Add the pumpkin. Mix in the pumpkin puree, heavy whipping cream, and vanilla extract.
4. Add the dry ingredients. Add the almond flour, coconut flour, pumpkin pie spice, and baking powder. Stir until everything is evenly combined. Set the batter aside while you prepare the filling.
5. Make the cheesecake filling. Add the softened cream cheese, egg, sweetener, almond flour, and vanilla extract to a separate bowl. Mix until smooth and no lumps remain.
6. Assemble the muffins. Divide the pumpkin batter among the muffin cups, filling each about halfway. Add about 1 tablespoon of cheesecake filling to each muffin, then top with about 1 tablespoon more pumpkin batter.
7. Swirl the filling. Use a toothpick to gently swirl the cheesecake filling into the pumpkin batter.
8. Bake. Bake at 350°F (180°C) for about 20 minutes, or until the muffin tops are set and a toothpick inserted into the pumpkin portion comes out clean or with a few moist crumbs.
9. Cool. Remove the muffins from the oven and transfer them to a cooling rack. Let them cool before serving.

Recipe Variations

• Once cooled, drizzle the muffins with your favorite sugar-free caramel sauce.
• Fold some sugar-free chocolate chips into the pumpkin batter.
• Add chopped pecans or walnuts for extra crunch.
• Sprinkle a little extra pumpkin pie spice over the tops before baking for even more fall flavor.

How to Store Pumpkin Cheesecake Muffins

Because these muffins contain a cream cheese filling, they should be refrigerated once cooled.

Refrigerator: Store the muffins in an airtight container in the refrigerator for up to 4–5 days.

Freezer: Wrap each cooled muffin individually, then place them in a freezer-safe bag or container. Freeze for up to 2 months.

Thaw frozen muffins overnight in the refrigerator or let them come to room temperature before serving. You can warm them briefly in the microwave if you prefer them slightly warm.

Frequently Asked Questions

More Pumpkin Recipes

• Pumpkin Pie Spice Recipe
• Keto Pumpkin Mousse
• Creamy Keto Pumpkin Soup
• Keto Pumpkin Pie

Keto Pumpkin Cheesecake Muffins

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Prep time 10 minutes mins

Cook Time 20 minutes mins

Yields 12 servings

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Description

 

These keto pumpkin cheesecake muffins are soft, moist, and packed with warm pumpkin spice, with a creamy cheesecake swirl in every muffin. They take just 10 minutes to prep and about 20 minutes to bake, making them an easy low-carb fall breakfast or dessert.

Ingredients

 

US CustomaryMetric

 

1x2x3x

For the muffins batter

• 5 eggs room temperature
• 2 cups almond flour
• 2 tbsp coconut flour
• ¾ cup pumpkin puree
• 2-3 tsp pumpkin pie spice
• 3 tbsp heavy whipping cream
• 3/4 cup sweetener
• 4 tbsp butter softened
• 1 tsp vanilla extract
• 1 1/2 tsp baking powder

For the cheesecake filling

• 4 oz cream cheese softened
• 1 large egg
• 1/4 cup sweetener
• 2 tbsp almond flour
• 1 tsp vanilla extract

Instructions

 

• Preheat the oven to 350°F (180°C) and line a 12-cup muffin pan with paper or silicone liners.
• Add the eggs, melted and slightly cooled butter, and sweetener to a large mixing bowl. Whisk until smooth and well combined.
• Mix in the pumpkin puree, heavy whipping cream, and vanilla extract.
• Add the almond flour, coconut flour, pumpkin pie spice, and baking powder. Stir until evenly combined, then set the batter aside.
• Make the cheesecake filling. Add the softened cream cheese, egg, sweetener, almond flour, and vanilla extract to a separate mixing bowl. Mix until smooth and lump-free.
• Divide the pumpkin batter among the prepared muffin cups, filling each about halfway.
• Add about 1 tablespoon of cheesecake filling to each muffin, then top with about 1 tablespoon more pumpkin batter.
• Use a toothpick to gently swirl the cheesecake mixture into the pumpkin batter.
• Bake in the preheated oven for 20 minutes, or until the tops are set and a toothpick inserted into the pumpkin portion comes out clean or with a few moist crumbs.
• Remove the muffins from the oven and transfer them to a cooling rack. Allow them to cool before serving.

Nutrition Facts

Amount per serving.

Calories

236kcal

Total Carbs

7g

Net Carbs

Protein

8g

Fat

21g

Fiber

3g

Sugar

2g

How do we calculate the nutrition info?

These nutrition facts listed are determined using nutrition information from the USDA Food Database. Our nutrition facts are accurate, but if you are using different products, please make your calculations. Net carb count is calculated by subtracting both fiber and sugar alcohols because they don’t raise blood sugar.

Course Dessert

Cuisine American

Keyword Keto Pumpkin Cheesecake Muffins

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