Keto Pumpkin Cheesecake Muffin Bites

Section: Midday Bowls & Handhelds with Momentum

These bites offer a perfect balance of rich cream cheese and spiced pumpkin, swirled together for a moist, tender result. With keto-friendly sweeteners and warming spices, they’re ideal for satisfying a dessert craving while keeping carbs low. Quick to prep and perfect for autumn, these muffin bites become even better after chilling, yielding a creamy, decadent texture. Enjoy them with a sprinkle of pecans or paired with coffee for an easy, guilt-free snack or ending to a meal.

A woman wearing an apron and smiling.
Authored by Clara
Last revised on Wed, 24 Sep 2025 18:05:24 GMT
A slice of pumpkin cheesecake muffin bites. Save
A slice of pumpkin cheesecake muffin bites. | zetluna.com

Creamy cheesecake muffin bites swirled with golden pumpkin and a cozy blend of spices deliver all the flavors of fall in a keto friendly treat. These are perfect for anyone craving something sweet yet mindful of carbs and sugar. The gentle tang of cream cheese and the warmth of cinnamon and nutmeg make them a favorite for autumn snacking or an after dinner dessert you can feel good about.

I remember making these when I first started keto and desperately missed the flavors of pumpkin pie. They filled my kitchen with the scent of fall and quickly became my go to snack to share with friends at work.

Ingredients

  • Cream cheese: Use full fat for best texture and flavor Make sure it is softened for smooth mixing
  • Powdered erythritol or your favorite keto sweetener: Ensures sweetness without carbs Choose fine powdered form for seamless blending
  • Large eggs: Bind everything together and add richness Fresh eggs from local sources taste best if you can get them
  • Vanilla extract: Adds depth and natural aroma Opt for pure vanilla not imitation
  • Pumpkin purée: Choose unsweetened not pumpkin pie filling Canned or homemade works as long as it is smooth
  • Ground cinnamon: Gives the muffins their classic warmth Fresh or recently opened spices bring boldness
  • Ground nutmeg: Offers nutty autumn notes Freshly grated or from a quality jar
  • Ground ginger: Adds gentle heat and depth Look for fragrant ginger powder for punch
  • Ground cloves: Just a pinch is enough for spicy backbone Store cloves tightly sealed for freshness
  • Salt: Enhances all flavors A fine sea salt works especially well
  • Chopped pecans: Optional for nutty crunch Toasted pecans give a richer flavor If you prefer you can use walnuts or omit for nut free
  • Extra cinnamon: Optional for dusting over the tops

Instructions

Prep the Tin:
Line a 12 cup mini muffin tin with paper liners or lightly grease each cup This helps with easy removal and prevents sticking
Mix the Cheesecake Base:
In a medium bowl use an electric mixer or sturdy whisk to beat cream cheese with powdered erythritol Mix until you have a creamy lump free texture Add in the egg and vanilla then beat again until the mixture is fully blended and silky Set aside
Make the Pumpkin Swirl:
In a separate bowl whisk pumpkin purée with egg powdered erythritol cinnamon nutmeg ginger cloves and a pinch of salt Whisk until the mixture looks even and smooth with no streaks of egg white
Layer and Swirl:
Add roughly one tablespoon of cheesecake mixture to each muffin cup Follow with one tablespoon of the pumpkin mixture Use a clean toothpick or skewer to lightly swirl them together The marbling is both pretty and gives a blend of both flavors in every bite
Add Topping:
If you like sprinkle chopped pecans and a small shake of cinnamon over each muffin bite The pecans toast lightly as they bake and add wonderful crunch
Bake Until Just Set:
Slide the tin into your preheated oven at 350 degrees Fahrenheit Bake for 16 to 18 minutes Check that the tops are set but still slightly jiggly in the center A toothpick should come out mostly clean but not bone dry
Cool and Chill:
Let the muffin bites cool in the tin for at least 10 minutes Then gently transfer them to a wire rack to finish cooling To ensure the ultimate creamy texture chill in the fridge for one hour before serving
A plate of food with a fork on it.
A plate of food with a fork on it. | zetluna.com

I always look forward to swirling together the cheesecake and pumpkin layers The patterns are never the same twice and my kids love helping with this part It makes for a fun family kitchen moment every time

Storage Tips

Store your muffin bites in an airtight container in the fridge for up to five days For longer storage freeze in a single layer until solid then pop into a freezer safe container They thaw quickly in the fridge or at room temperature

Ingredient Substitutions

If you are out of pecans try walnuts sunflower seeds or skip the nuts entirely For the sweetener use any powdered keto blend you like Monk fruit blends are just as tasty If you love extra spice add a pinch more ginger or cloves

Serving Suggestions

These muffin bites go well with a mug of black coffee or cinnamon tea For a holiday tray add keto whipped cream or a dusting of extra spice Serve chilled for best results but they taste great straight from the fridge or cool room temperature

Cultural and Historical Context

Pumpkin baked goods are a beloved part of American autumn traditions The combination of creamy cheesecake and pumpkin pie flavors brings together two classic desserts in one keto friendly bite During pumpkin season these are just as welcome at family gatherings as the classic pie

Seasonal Adaptations

In spring try swirling with lemon zest instead of pumpkin In winter dust the tops with a pinch of extra ginger Summer versions can use mashed berries or swirl in a little unsweetened cocoa powder Use fresh pumpkin purée when available for deeper color and taste Swap pecans for toasted pepitas in fall for extra crunch Stick with classic spices for a true autumn effect

Success Stories

Many readers have shared that these muffin bites satisfy their pumpkin dessert cravings while staying on track with keto One friend brings them to potlucks and they always disappear first Another says the recipe helped her stick to low carb foods over the holidays and she did not miss regular pie at all

Freezer Meal Conversion

Let the bites cool fully then freeze them in a single layer Once solid stack with parchment paper between layers in a tight lidded container They keep well for up to two months Defrost in the fridge for creamy texture

A slice of cake with walnuts on top.
A slice of cake with walnuts on top. | zetluna.com

With their cozy swirl and creamy bite these muffin treats bring the best flavors of fall to your table. You will love every guilt free mouthful whether for dessert or snack.

Common Questions About Recipes

→ How can I ensure the swirls come out distinct in each muffin bite?

Use a toothpick or skewer to gently mix the pumpkin and cheesecake layers, being careful not to over-blend for a defined swirl.

→ Can a different sweetener be used instead of erythritol?

Yes, most keto-friendly powdered sweeteners will work; just ensure they blend smoothly and maintain a similar sweetness level.

→ Do these muffin bites need to be refrigerated after baking?

Absolutely. Chilling helps set the texture, making the bites creamy and holding the swirls intact. Store them in the fridge for best results.

→ How can I make a nut-free version?

Simply omit the pecan topping or use a nut-free alternative. The base flavors will still be rich and satisfying.

→ Is canned pumpkin purée or fresh pumpkin better for this?

Unsweetened canned pumpkin purée offers consistency and ease, but well-drained fresh purée can also be used.

Keto Pumpkin Cheesecake Muffin Bites

Soft, creamy bites swirled with spiced pumpkin and cheesecake make a guilt-free keto-friendly autumn treat.

Prep Time
15 mins
Time to Cook
18 mins
Overall Time
33 mins
Authored by: Clara

Recipe Type: Orbit Fuel

Skill Level Required: Beginner-Friendly

Cuisine Type: American

Recipe Output: 12 Number of Portions (12 muffin bites)

Dietary Needs: Low-Carbohydrate, Veggie-Friendly, Free of Gluten

The Ingredients You'll Need

→ Cheesecake Layer

01 8 ounces cream cheese, softened
02 1/4 cup powdered erythritol or preferred keto sweetener
03 1 large egg
04 1/2 teaspoon vanilla extract

→ Pumpkin Layer

05 1/2 cup pumpkin purée, unsweetened, not pie filling
06 1 large egg
07 2 tablespoons powdered erythritol or preferred keto sweetener
08 1/2 teaspoon ground cinnamon
09 1/4 teaspoon ground nutmeg
10 1/4 teaspoon ground ginger
11 1/8 teaspoon ground cloves
12 Pinch of salt

→ Optional Topping

13 2 tablespoons chopped pecans, optional
14 1/2 teaspoon ground cinnamon, optional

Step-by-Step Instructions

Step 01

Preheat oven to 350°F. Line a 12-cup mini muffin tin with paper liners or lightly grease each cup.

Step 02

In a medium mixing bowl, beat cream cheese with powdered erythritol using an electric mixer or whisk until smooth. Add the egg and vanilla extract, blending until fully incorporated. Set aside.

Step 03

In a separate bowl, whisk together pumpkin purée, egg, erythritol, cinnamon, nutmeg, ginger, cloves, and salt until mixture is smooth and uniform.

Step 04

Spoon approximately 1 tablespoon of the cheesecake mixture into each prepared muffin cup, followed by 1 tablespoon of the pumpkin mixture. Use a toothpick or skewer to gently swirl the two layers for a marbled effect.

Step 05

If desired, sprinkle each muffin with chopped pecans and a pinch of ground cinnamon.

Step 06

Bake in the preheated oven for 16 to 18 minutes, or until centers are just set and a toothpick inserted in the center comes out mostly clean.

Step 07

Allow to cool in the pan for 10 minutes, then transfer muffins to a wire rack to cool completely. For best texture, chill in the refrigerator for at least 1 hour prior to serving.

Additional Notes

  1. For a nut-free version, omit pecans or substitute with chopped walnuts if desired.
  2. A tablespoon of sour cream can be incorporated in the cheesecake layer for added creaminess.
  3. Serving chilled enhances both texture and flavor.
  4. Pair with coffee or herbal tea for a complementary experience.

Tools You'll Need

  • Mini muffin tin, 12-cup capacity
  • Mixing bowls
  • Electric mixer or whisk
  • Measuring spoons and cups
  • Toothpick or skewer

Allergy Information

Review each ingredient to identify allergens and consult an expert if needed.
  • Contains dairy (cream cheese) and egg.
  • Contains nuts if pecan topping is used.
  • Keto sweeteners may contain allergens; verify product labeling if necessary.

Nutritional Facts (Per Serving)

Keep in mind these details are for general guidance and shouldn't replace professional advice.
  • Caloric Content: 70
  • Fats: 6 grams
  • Carbohydrates: 2 grams
  • Proteins: 2 grams