Keto Pumpkin Cheesecake Muffins

There’s something magical about baking when the leaves start to fall. The scent of warm spices and creamy pumpkin drifting through the kitchen just makes everything feel softer, slower — more sacred. I still remember the first time I whipped up a batch of keto pumpkin cheesecake muffins for a chilly Sunday brunch with my sister. We stood barefoot by the oven, coffee mugs in hand, waiting for the timer to chime. That first bite — tender cookie crust, luscious pumpkin filling, and the gentle spice of fall — sealed the moment into memory.

These muffins aren’t just sugar-free and low-carb — they’re downright craveable. You get all the indulgence of a creamy pumpkin cheesecake, but in handheld form, with none of the guilt. It’s the kind of recipe you’ll find yourself making on repeat — whether for cozy gatherings or just because you need a little something sweet after dinner.

Let’s make memories one bite at a time.

Why You’ll Love This Recipe

These keto pumpkin cheesecake muffins bring all the flavor and comfort of traditional pumpkin pie, but with a light, portable twist. You get soft almond flour cookie crusts holding in creamy, spiced pumpkin cheesecake — each bite rich but not heavy.

They’re naturally gluten-free and keto-friendly, making them perfect for anyone watching carbs or sugar. With under 5g net carbs per serving, they fit beautifully into any low-carb lifestyle.

This recipe is surprisingly easy to master, even for beginner bakers. No complicated water baths or crust chilling — just mix, bake, and fill. Ready in under 45 minutes from start to finish!

Great for fall brunches, holiday dessert tables, or as a snack to enjoy with your pumpkin spice latte. Kids love the mini size, and adults appreciate the clean ingredients.

The best part? These keto pumpkin cheesecake muffins keep well in the fridge and taste even better the next day. One batch, many cozy moments.

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Ingredient Overview

These muffins are warm, creamy, and loaded with comforting fall flavor — all while staying low in carbs and sugar. The almond flour cookie base gives structure and crunch, while the no-bake pumpkin cheesecake mousse adds luscious, silky contrast.

• Almond Flour: A grain-free base that gives the cookie crust a nutty, rich flavor and a tender texture.

• Swerve Brown & Confectioners: Natural sugar substitutes that add sweetness and moisture without spiking blood sugar.

• Pumpkin Puree: Adds authentic fall flavor and beautiful orange hue — be sure to use pure pumpkin, not pie filling.

• Cream Cheese: The key to our velvety, tangy cheesecake filling. Softened to ensure smooth mixing.

• Heavy Whipping Cream: Adds airiness and fluff to the mousse — beat until stiff peaks for best results.

• Pumpkin Pie Spice: Brings warm notes of cinnamon, ginger, cloves, and nutmeg — perfect for fall.

• Butter: Melted into the crust for richness and cohesion.

• Egg White: Helps bind the cookie dough into firm little cups.

• Vanilla Extract: Enhances every other flavor with a soft, fragrant sweetness.

Tip: Garnish the tops with a sprinkle of pumpkin pie spice or sugar-free sprinkles for festive flair!

Step-by-step Instructions

Step 1: Preheat and Prep Your Pan

Start by preheating your oven to 325°F. Line a mini muffin pan with 24 silicone liners — this helps the keto pumpkin cheesecake muffins pop out cleanly without sticking. If you’re using a silicone muffin pan, you can skip the liners.

Step 2: Mix the Dry Ingredients

In a large bowl, whisk together the almond flour, Swerve Brown, ginger, cinnamon, baking soda, salt, and cloves. These spices give your muffin cups that warm fall flavor base.

Step 3: Stir in Wet Ingredients

Add the melted butter, egg white, and vanilla extract into the dry mix. Stir well until the dough is moist and sticks together easily. You want it pliable, but not too sticky.

Step 4: Form the Cookie Cups

Roll the dough into ¾-inch balls. Place one in each muffin well and press gently up the sides to create little crust cups. Be sure they’re even so they bake consistently.

Tip: Use a measuring spoon or your thumb to make uniform wells — it helps hold the filling better later!

Step 5: Bake Until Golden

Slide the pan into the oven and bake for 15–20 minutes. They should puff slightly and turn golden brown at the edges. Remove and let them cool for 10 minutes.

Step 6: Reshape the Centers

Once they’ve cooled a bit, gently press the centers back down using a spoon or your thumb to deepen the wells. Let them cool completely before filling.

Step 7: Whip the Cheesecake Base

In a clean bowl, beat together softened cream cheese and Swerve Confectioners until smooth. Add in pumpkin puree, pumpkin pie spice, and vanilla. Keep mixing until the filling is creamy and uniform.

Step 8: Fold in Whipped Cream

Whip your heavy cream separately until it holds stiff peaks. Gently fold it into the pumpkin cheesecake mix. Don’t overmix — you want to keep the air in it!

Step 9: Fill the Muffin Cups

Transfer the filling to a piping bag or use a spoon to fill each cookie cup generously. Swirl it on top if you like — it makes your keto pumpkin cheesecake muffins look bakery-worthy.

Step 10: Decorate and Chill

Finish with a dusting of pumpkin pie spice or sugar-free sprinkles. Chill the muffins for at least 20 minutes so the filling sets properly before serving.

Now that your dish is coming together beautifully, let’s explore some pro tips and creative variations!

Pro Tips

For the best flavor and texture in your keto pumpkin cheesecake muffins, always use room temperature cream cheese. Cold cream cheese won’t blend smoothly and can leave your filling lumpy.

If your cookie cups puff up too much during baking, don’t worry — just press down the centers gently with the back of a spoon while they’re still warm to maintain space for the filling.

Use a piping bag with a star tip for that polished, bakery-style swirl on top. It makes the keto pumpkin cheesecake muffins look extra festive, especially for fall gatherings or holiday dessert trays.

Planning ahead? You can bake the cookie cups a day in advance and store them in an airtight container. Then fill them just before serving for optimal freshness and structure.

For extra flair, link your flavors together by serving them alongside something cozy like this creamy Pumpkin Fluff Dip. Both treats capture that autumn warmth with minimal sugar.

Variations

Want a nut-free version of these keto pumpkin cheesecake muffins? Swap almond flour for sunflower seed flour in equal amounts — it offers a similar texture with no nuts involved.

For a touch of chocolate, try adding a teaspoon of cocoa powder to the cookie crust mixture. It pairs beautifully with the pumpkin spice filling and gives the muffins a rich depth.

Make them extra festive by adding sugar-free chocolate chips or chopped pecans into the crust dough. This gives a fun crunch and even more texture in every bite.

You can also pipe the filling into store-bought keto cookie shells if you’re in a hurry. While homemade crusts are amazing, sometimes shortcuts save the day!

For more fall baking inspiration, check out these healthy pumpkin oat cookies — they’re another reader favorite when you’re craving that seasonal flavor.

Frequently Asked Questions

Serving Suggestions

These keto pumpkin cheesecake muffins are just the thing to bring along to a crisp autumn brunch or cozy holiday party. Serve them with a steaming mug of coffee or your favorite low-carb chai for a comforting midday treat. If you’re feeling festive, they pair beautifully with Pumpkin Cream Cold Brew for that full café-at-home vibe. You can also tuck them into a fall-themed dessert board with fresh berries, nuts, and dark chocolate chunks. However you serve them, these muffins are sure to make hearts (and taste buds) happy.

Conclusion

There’s something deeply satisfying about a dessert that delivers indulgence without compromise — and these keto pumpkin cheesecake muffins do exactly that. They bring together warm spice, creamy filling, and cookie-like crunch in every little bite. Whether you’re following keto strictly or simply love better-for-you treats, this recipe fits right in. You get that sense of occasion, the kind you usually save for big cakes or pies, but without the fuss.

And if you’re looking to explore even more seasonal indulgence, don’t miss what we’ve got simmering over in the desserts category. You’ll find flavor-packed inspiration to keep your oven busy all season long.

Ready to bake your batch of keto pumpkin cheesecake muffins? I’d love to hear how they turn out in your kitchen! Drop a comment below, share a photo on social media, or tag us so we can celebrate your creation. Your twist on the recipe might just inspire someone else.

From my kitchen to yours — happy baking, friend!
And don’t forget to check out what’s cookin’ on our Pinterest for more cozy fall bites and creative kitchen magic.