If you’re hunting for a deliciously guilt-free treat that bursts with warm autumn flavors, the Keto Pumpkin Cheesecake Muffin Bites Recipe is your new best friend. These little gems combine the creamy richness of cheesecake with the cozy spices of pumpkin, all while keeping it low-carb and keto-friendly. Perfectly portioned, delightfully moist, and subtly sweet, they’re the snack or breakfast that feels indulgent but won’t derail your keto lifestyle. I can’t wait to share how simple ingredients come together to make something truly special!

Ingredients You’ll Need
Gathering your ingredients for this recipe is a breeze, and each one plays a crucial role in creating the perfect texture and flavor balance. From the velvety cream cheese to the spiced pumpkin puree, these staples work together to deliver a muffin bite that’s both satisfying and irresistible.
- Cream cheese (8 ounces, softened): Adds creamy richness and smooth texture essential for the cheesecake layer.
- Powdered erythritol (1/4 cup + 2 tablespoons): A keto-friendly sweetener that keeps things sweet without the sugar crash.
- Eggs (2 large): Provide structure and help bind the two mixtures together.
- Vanilla extract (1/2 teaspoon): Enhances sweetness and adds a lovely aromatic dimension.
- Pumpkin purée (1/2 cup, unsweetened): Brings natural pumpkin flavor and moisture, making the bites tender and spiced.
- Ground cinnamon (1/2 teaspoon + optional pinch): Injects warm, inviting spice that’s perfect for fall.
- Ground nutmeg (1/4 teaspoon): Adds a subtle nutty spice for depth.
- Ground ginger (1/4 teaspoon): Offers a gentle kick that complements the pumpkin.
- Ground cloves (1/8 teaspoon): Intensifies the spice blend with a sweet and slightly peppery note.
- Pinch of salt: Balances the sweetness and enhances all flavors.
- Chopped pecans (2 tablespoons, optional): Provides a delightful crunch and nutty contrast.
How to Make Keto Pumpkin Cheesecake Muffin Bites Recipe
Step 1: Preheat and Prepare Your Pan
Start by preheating your oven to 350°F, ensuring it reaches the perfect temperature for baking these delicate bites. Line a 12-cup mini muffin tin with paper liners or lightly grease each cup to prevent sticking—this prep step makes retrieval a breeze and keeps your muffin bites intact.
Step 2: Make the Cream Cheese Mixture
In a medium bowl, beat the softened cream cheese with powdered erythritol until smooth and fluffy. This creamy base is the heart of your cheesecake layer, so take a moment to ensure it’s perfectly blended. Add one egg and vanilla extract, then mix again until fully incorporated—this will give your bites that melt-in-your-mouth cheesecake sensation.
Step 3: Create the Pumpkin Mixture
In a separate bowl, whisk together the pumpkin puree, the remaining egg, powdered erythritol, cinnamon, nutmeg, ginger, cloves, and a pinch of salt. This spice-laden pumpkin mix brings the warm, comforting flavor that screams fall, while the erythritol keeps things keto-approved. Mixing until smooth ensures even spice distribution throughout each bite.
Step 4: Layer and Swirl
Spoon about one tablespoon of the cheesecake mixture into each muffin cup, followed by one tablespoon of the pumpkin mixture. Using a toothpick or skewer, gently swirl the two layers to create a beautiful marbled effect. This not only looks stunning but promises a perfect bite of cheesecake and pumpkin in every mouthful.
Step 5: Add Toppings and Bake
If you love a bit of crunch, sprinkle the tops with chopped pecans and a pinch of ground cinnamon. Then bake in your preheated oven for 16 to 18 minutes, until the centers are just set and a toothpick inserted comes out mostly clean. These muffin bites puff up slightly while baking but settle into irresistibly moist treats.
Step 6: Cool and Chill
Allow the muffin bites to cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely. For the best texture and flavor, refrigerate them for at least one hour. Chilling lets the cheesecake layer firm up perfectly, enhancing the bite and making them ideal for enjoying straight from the fridge.
How to Serve Keto Pumpkin Cheesecake Muffin Bites Recipe

Garnishes
Sprinkling a pinch of extra ground cinnamon or a light dusting of keto-friendly powdered sweetener after chilling can add a lovely finishing touch. Freshly whipped cream or a dollop of sugar-free pumpkin spice whipped topping elevates these bites into a decadent treat suitable for any occasion.
Side Dishes
Pair these muffin bites with a warm cup of herbal tea, black coffee, or your favorite keto latte for a cozy snack moment. If serving breakfast, a side of fresh berries or a simple green salad can complement their richness beautifully while keeping the meal low-carb.
Creative Ways to Present
Turn these muffin bites into bite-sized desserts on a festive platter garnished with toasted pecans and mint leaves. For brunch, stack a few on a pretty plate with a drizzle of sugar-free caramel sauce or cream cheese glaze for an irresistible display that will wow your guests.
Make Ahead and Storage
Storing Leftovers
These Keto Pumpkin Cheesecake Muffin Bites keep incredibly well in an airtight container in the refrigerator for up to 5 days. Keeping them cold helps maintain the creamy texture of the cheesecake and the moist pumpkin flavor, so you can enjoy them throughout the week without sacrificing taste or quality.
Freezing
If you want to plan ahead, these muffin bites freeze beautifully! Place them in a single layer on a baking sheet to freeze initially, then transfer to a freezer-safe bag or container. They can stay frozen for up to 2 months, making it easy to enjoy a quick keto-friendly treat anytime.
Reheating
To enjoy after freezing, thaw overnight in the refrigerator, then warm slightly in the microwave for 15-20 seconds if you prefer them soft and cozy. Alternatively, enjoy them chilled—either way, the flavors and texture hold up wonderfully whether cold or warmed.
FAQs
Can I use a different sweetener instead of erythritol?
Absolutely! You can swap powdered erythritol for any keto-friendly powdered sweetener, such as monk fruit or stevia blends. Just adjust the quantity according to sweetness preference and sweetness level of your chosen sweetener.
Are these muffin bites dairy-free?
They are not, due to the cream cheese which is essential for the cheesecake texture. For a dairy-free variation, you might experiment with a firm coconut cream or cashew-based cream cheese alternative, although results may vary.
Can I make these into full-sized muffins?
Yes, but baking times will increase. Use a standard muffin tin and bake for about 25-30 minutes, checking doneness with a toothpick. The texture might be slightly different but still delicious.
Is pumpkin pie spice the same as the spice mix used here?
Pumpkin pie spice typically includes cinnamon, nutmeg, ginger, and cloves—the same spices used in this recipe. You can substitute the individual measurements with about 1 teaspoon of pumpkin pie spice for simplicity.
How do I know when the muffin bites are done baking?
They are ready when the centers are just set but still slightly soft, and a toothpick inserted comes out mostly clean with a few moist crumbs. Overbaking can dry them out, so keep a close eye during the last few minutes.
Final Thoughts
The Keto Pumpkin Cheesecake Muffin Bites Recipe is truly a celebration of fall flavors made keto-friendly without compromising on indulgence. They’re perfect for a snack, breakfast, or even a dessert treat that you don’t have to feel guilty about. I’m so excited for you to try them—once you do, they’ll surely become your favorite little cozy bites to enjoy again and again.
Print
Keto Pumpkin Cheesecake Muffin Bites Recipe
- Prep Time: 10 minutes
- Cook Time: 18 minutes
- Total Time: 33 minutes
- Yield: 12 mini muffin bites 1x
- Category: Dessert
- Method: Baking
- Cuisine: American
- Diet: Diabetic
Description
These Keto Pumpkin Cheesecake Muffin Bites are a delicious low-carb treat combining creamy cheesecake and spiced pumpkin layers swirled together in perfectly bite-sized muffins. Sweetened with erythritol, they are ideal for a keto diet and make a wonderful snack or dessert during the fall season.
Ingredients
Cheesecake Layer
- 8 ounces cream cheese, softened
- 1/4 cup powdered erythritol or preferred keto sweetener
- 1 large egg
- 1/2 teaspoon vanilla extract
Pumpkin Layer
- 1/2 cup pumpkin purée, unsweetened, not pie filling
- 1 large egg
- 2 tablespoons powdered erythritol or preferred keto sweetener
- 1/2 teaspoon ground cinnamon
- 1/4 teaspoon ground nutmeg
- 1/4 teaspoon ground ginger
- 1/8 teaspoon ground cloves
- Pinch of salt
Toppings (Optional)
- 2 tablespoons chopped pecans
- 1/2 teaspoon ground cinnamon
Instructions
- Preheat and prepare muffin tin: Preheat your oven to 350°F (175°C). Line a 12-cup mini muffin tin with paper liners or lightly grease each cup to prevent sticking.
- Make the cheesecake mixture: In a medium mixing bowl, use an electric mixer or whisk to beat the softened cream cheese and powdered erythritol until smooth and creamy. Add one large egg and vanilla extract, blending until fully incorporated and silky.
- Prepare the pumpkin mixture: In a separate bowl, whisk together the pumpkin purée, egg, erythritol, cinnamon, nutmeg, ginger, cloves, and a pinch of salt. Whisk until the mixture is smooth and well combined.
- Layer the mixtures in muffin cups: Spoon about 1 tablespoon of the cheesecake mixture into each prepared muffin cup, then add 1 tablespoon of the pumpkin mixture on top. Use a toothpick or skewer to gently swirl the two layers together, creating a marbled effect without overmixing.
- Add toppings: If desired, sprinkle each muffin with chopped pecans and a pinch of ground cinnamon for added texture and flavor.
- Bake: Place the muffin tin in the preheated oven and bake for 16 to 18 minutes. The muffins are done when the centers are just set and a toothpick inserted comes out mostly clean.
- Cool and chill: Allow the muffins to cool in the pan for 10 minutes, then transfer them to a wire rack to cool completely. For the best texture and flavor, chill the muffins in the refrigerator for at least 1 hour before serving.
Notes
- If you prefer a sweeter muffin, adjust the erythritol amount to taste.
- Make sure to use unsweetened pumpkin purée, not pumpkin pie filling, to control sugar content.
- Swirling should be gentle to maintain distinct layers and marbled appearance.
- Chilling the muffins improves texture and helps flavors meld.
- Store leftovers in an airtight container in the refrigerator for up to 5 days.
- These muffin bites can be frozen for up to 2 months; thaw overnight in the refrigerator before serving.

