Keto Pumpkin Cheesecake Muffins

I still remember the first chilly Saturday of October last year. The air had that crisp, cinnamon-snap feel, and my youngest had just begged for something “cakey but not too sweet” for breakfast. I pulled out the almond flour, a brick of cream cheese, and an open can of pumpkin puree from the fridge. That morning, these Keto Pumpkin Cheesecake Muffins came to life, and friends, they didn’t last past noon.

Each bite of these moist, warmly spiced muffins is like wrapping your hands around a mug of spiced chai. You’ve got layers of fall flavor — from the creamy cheesecake swirl tucked right in the center to the buttery almond flour streusel scattered on top. And because they’re low-carb, they’re the perfect guilt-free treat whether you’re curled up by the fire or heading out for a leaf-peeping drive.

Let’s make memories one bite at a time.

Why You’ll Love This Recipe

You’ll love these Keto Pumpkin Cheesecake Muffins for more than just their stunning swirl. They bake up tender and moist, with rich pumpkin flavor in every bite. The creamy cheesecake center turns each muffin into a delightful little surprise.

They’re easy enough for weekday prep but impressive enough for a fall brunch. And if you’re following a low-carb or keto lifestyle? These muffins will feel like a bakery indulgence without the sugar spike. Ready in under 30 minutes once your filling is prepped, they’re a breeze to assemble and perfect for storing or freezing ahead.

With warm pumpkin spice and just the right touch of cinnamon, this recipe offers cozy comfort with keto-friendly macros.

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Ingredient Overview

These Keto Pumpkin Cheesecake Muffins blend fall spice, creamy texture, and just a hint of decadence — all while keeping carbs in check. They’re rich but not heavy, thanks to balanced ingredients that deliver both structure and flavor.

• Almond flour: The star of our keto base, bringing moisture and nutty depth.

• Coconut flour: Just enough to give the muffins structure and a tender crumb.

• Pumpkin puree: Pure canned pumpkin (not pie filling) adds seasonal richness and velvety moisture.

• Cream cheese: A full-fat block works best here, creating a silky cheesecake center.

• Granulated sugar substitute: Keeps it sweet without the carbs — monk fruit or erythritol work well.

• Psyllium husk powder: Helps hold everything together while adding fiber.

• Pumpkin spice & cinnamon: The cozy duo that makes these muffins unmistakably fall.

• Butter: Adds richness to both the batter and that irresistible streusel topping.

Food styling tip: Once cooled, dust the tops with a sprinkle of cinnamon or serve with a dollop of whipped cream for a little extra flair.

Step-by-step Instructions

Step-by-Step Instructions

Step 1: Prepare the Cheesecake Filling

Start by making the creamy heart of your Keto Pumpkin Cheesecake Muffins. In a medium bowl, beat the softened cream cheese, confectioner’s sugar substitute, and vanilla extract using an electric mixer. Mix until smooth and fluffy. Shape the mixture into a log about 1¼ inches thick, wrap it in cling film or wax paper, and place it in the freezer. Let it firm up for about 1½ hours so it slices cleanly later.

Step 2: Mix the Muffin Batter

While the filling chills, preheat your oven to 350°F and line two muffin tins with 24 cupcake liners. In a large bowl, cream the softened butter and sugar substitute until light and airy. Beat in the eggs one at a time, then stir in the pumpkin puree and vanilla. Next, mix in the almond flour, coconut flour, baking powder, psyllium husk powder, salt, cinnamon, ginger, and pumpkin spice. The aroma alone will have you dreaming of fall!

Step 3: Make the Streusel Topping

In a small bowl, combine almond flour, coconut flour, cinnamon, pumpkin spice, sugar substitute, and sea salt. Add the cold, thinly sliced butter. Using two forks (or clean hands), cut the butter into the dry mixture until it resembles coarse crumbs. This streusel adds the final bakery-style touch to your Keto Pumpkin Cheesecake Muffins.

Step 4: Assemble the Muffins

Spoon about 2 tablespoons of batter into each muffin liner to cover the bottom. Remove the cheesecake log from the freezer and slice it into 24 even rounds. Place one slice into each muffin well, right in the center. Cover the filling with more batter until just below the top of the liner. Sprinkle about 1 tablespoon of streusel over each one — don’t skimp!

Step 5: Bake Until Golden

Bake the muffins in your preheated oven for 20–25 minutes, or until the tops are golden and a toothpick inserted into the edge comes out clean. The cream cheese centers should be just set, with a soft swirl waiting inside each muffin.

Tip: Don’t open the oven too soon — let the muffins rise and set fully for that bakery-style dome.

Step 6: Cool and Store

Transfer the muffins to a wire rack and let them cool completely. This allows the cheesecake filling to firm up. These Keto Pumpkin Cheesecake Muffins store beautifully — up to 5 days in the fridge or freeze them for up to 3 weeks for a grab-and-go breakfast treat.

Pro Tips

Use a block of full-fat cream cheese, not whipped or tub-style. The firmer texture holds its shape during baking and gives your Keto Pumpkin Cheesecake Muffins that luscious, bakery-style swirl.

Chill the cheesecake filling long enough. If the log isn’t firm, slicing it cleanly becomes difficult, and the filling can melt into the batter unevenly. About 90 minutes in the freezer works well.

Measure your flours after sifting. Especially with almond and coconut flour, sifting prevents dense muffins. Don’t pack them into the measuring cup — it can throw off the delicate moisture balance in your Keto Pumpkin Cheesecake Muffins.

Avoid overmixing. Once you add the flours and spices, gently mix just until combined. This helps keep your muffins light and tender.

Store properly. These muffins are fridge-friendly! Keep them in an airtight container for up to 5 days. For longer storage, wrap individually and freeze. A quick warm-up brings them right back to life.

And for extra pumpkin magic, try browsing our pumpkin muffins recipe for flavor pairings and seasonal tweaks.

Variations

Want a nut-free version of these Keto Pumpkin Cheesecake Muffins? Swap the almond flour with sunflower seed flour in a 1:1 ratio. It’ll offer the same texture without the allergens.

For added crunch, mix chopped pecans or walnuts into the streusel topping. It gives the muffins a hearty bite and lovely contrast with the creamy center.

Love chocolate? A few sugar-free chocolate chips in the muffin batter or sprinkled on top of the streusel makes these muffins taste like dessert — still keto!

If you’re a protein lover, consider adding a scoop of unflavored or vanilla protein powder to the batter. Or pair with our pumpkin protein balls for a low-carb snack duo.

Feeling bold? Try a maple-flavored sugar substitute or pumpkin caramel drizzle over cooled muffins for an autumn café vibe — all while staying low-carb.

Frequently Asked Questions

Serving Suggestions

These Keto Pumpkin Cheesecake Muffins are pure fall comfort in muffin form — perfect with a warm mug of cinnamon tea or keto chai latte on a brisk morning. I love pairing them with savory eggs for breakfast, or setting them out with a soft cheese board and roasted nuts at brunch. For a festive fall table, try serving them alongside our cozy Pumpkin French Toast Casserole — it’s a flavor-packed combo that’ll impress any guest.

Hosting a weekend get-together or fall harvest brunch? Arrange the muffins on a wooden board with a small bowl of whipped cream cheese spread or keto maple butter for slathering. For something refreshing, a chilled glass of almond milk or pumpkin spice cold brew balances their richness just right.

They also make thoughtful gifts — wrap a few in parchment and tie with twine for a seasonal treat your friends will love.

Conclusion

There’s something undeniably joyful about pulling a warm batch of Keto Pumpkin Cheesecake Muffins from the oven. Maybe it’s the swirl of cream cheese tucked inside, or the buttery streusel that crunches just so. Or maybe it’s just knowing you’ve created something that’s as kind to your body as it is to your taste buds.

Whether you’re baking to nourish your family, prepping breakfasts for the week, or simply welcoming the cozy season with open arms, this recipe makes you feel like home. And if you’re craving more fall sweetness without the carbs, check out our velvety Pumpkin Fluff Dip — it’s a low-carb dream in every bite.

Ready to fill your kitchen with cinnamon and joy? Try these Keto Pumpkin Cheesecake Muffins and tell me how yours turn out! Leave a comment below, tag your creations on social, or pin the recipe to save for later. I’d love to see your spin on this cozy fall favorite.

And if you’re on Pinterest, come say hi over on our recipe board — I share fresh seasonal inspiration every week.

From my kitchen to yours — happy cooking, friends!