As the leaves begin to change and the air turns crisp, there’s nothing quite like the warm, inviting aroma of freshly baked treats wafting through my kitchen. Enter these Keto Pumpkin Cream Cheese Muffins—a low-carb baking dream that perfectly captures the essence of fall. With just 4 net carbs each, these delightful muffins are not only a guilt-free indulgence but also a fantastic way to savor the season. The combination of moist pumpkin goodness and a rich cream cheese swirl makes them an irresistibly fluffy snack that’s perfect for breakfast or a cozy afternoon pick-me-up. Trust me, you won’t miss the carbs! Ready to embrace the flavors of fall with me? Let’s dive into this deliciously healthy recipe!

Why You’ll Crave These Muffins?
Irresistible flavor: The blend of pumpkin, warm spices, and cream cheese creates a delightfully rich taste experience that captures the essence of fall.
Convenient baking: With just a few simple steps, these muffins come together quickly—perfect for busy mornings or last-minute gatherings.
Low-carb indulgence: At only 4 net carbs each, they satisfy sweet cravings without compromising your keto lifestyle.
Versatile treat: Enjoy them for breakfast, a snack, or even as a dessert; they fit seamlessly into any meal.
Crowd-pleaser: Whip these up for friends and family, and watch as everyone enjoys these moist, fluffy delights. They pair wonderfully with a steaming cup of coffee or tea!
Looking for more tasty keto inspiration? Check out my Keto Avocado Shrimp for a refreshing twist or treat yourself to my Keto Cobb Egg salad!
Keto Pumpkin Cheesecake Muffins Ingredients
• Dive into the deliciousness with these Keto Pumpkin Cheesecake Muffins!
For the Muffins
- Butter – Adds moisture and richness; make sure it’s at room temperature for easy mixing.
- Swerve Granular – A keto-friendly sweetener that keeps your muffins sweet without the carbs. Substitute with other keto sweeteners if needed.
- Eggs – Essential for binding and moisture; they provide the structure for your fluffy muffins.
- Pumpkin Puree – Brings that authentic fall flavor and moisture; opt for pure, unsweetened pumpkin puree for the best results.
- Vanilla Extract – Elevates the flavor profile; always use pure vanilla for the richest taste.
- Almond Flour – The low-carb base of the muffins, providing a delightful texture; can substitute with coconut flour, but adjust quantities.
- Pumpkin Pie Spice – Infuses warm, inviting spice notes; swap with a homemade mix of cinnamon, ginger, and nutmeg if needed.
- Baking Soda – Ensures fluffy muffins by helping them rise; check freshness for optimal results.
- Salt – Balances sweetness and enhances the flavor of the muffins.
For the Cream Cheese Filling
- Cream Cheese – The star of the show that creates a rich and creamy filling; make sure it’s room temperature for smooth blending.
- Powdered Erythritol – Keeps your filling sweet in line with keto guidelines; feel free to use other powdered sweeteners as a substitute.
Embrace the flavors of fall with these tempting Keto Pumpkin Cheesecake Muffins—where every bite is a warm hug for your taste buds!
Step‑by‑Step Instructions for Keto Pumpkin Cheesecake Muffins
Step 1: Preheat the Oven
Begin your baking adventure by preheating your oven to 350°F (175°C). While the oven heats, grab a 12-count muffin pan and either grease it generously with butter or line it with parchment paper. This will ensure that your Keto Pumpkin Cheesecake Muffins release easily after baking, resulting in beautiful, intact treats.
Step 2: Prepare the Cream Cheese Filling
In a small mixing bowl, combine cream cheese, powdered erythritol, and vanilla extract. Using a hand mixer or a sturdy spatula, beat the ingredients together until the mixture is smooth and creamy, resembling a thick frosting. Set this delightful cream cheese filling aside for now; it will provide that delicious swirl in your muffins later on.
Step 3: Make the Muffin Batter
In a large mixing bowl, cream together the room temperature butter and Swerve granular sweetener. Beat them until the mixture is light and fluffy, about 3-5 minutes. Gradually add in the eggs, pumpkin puree, and vanilla extract, mixing until well combined. You’ll notice a beautiful, creamy mixture coming together—this is the base for your Keto Pumpkin Cheesecake Muffins.
Step 4: Combine Dry Ingredients
Next, gently incorporate the dry ingredients by adding almond flour, pumpkin pie spice, baking soda, and salt to your wet mixture. Stir carefully until just combined, ensuring you don’t overmix. The batter should be thick and slightly lumpy, bursting with the warm smells of fall.
Step 5: Fill the Muffin Tins
Using a spoon or a cookie scoop, divide the muffin batter evenly among the prepared muffin cups. Fill each cavity about two-thirds full to allow room for rising. Now, take the cream cheese filling you prepared earlier and add a tablespoon on top of each muffin batter.
Step 6: Create a Swirl
With a fork, gently swirl the cream cheese filling into the muffin batter, creating an inviting marbled effect. Don’t worry about making it perfect; the rustic look adds to the charm of your Keto Pumpkin Cheesecake Muffins.
Step 7: Bake the Muffins
Pop your muffin pan into the preheated oven and bake for about 25 minutes. Keep an eye on them; they’re ready when a toothpick inserted into the center comes out clean. The tops should have a lovely golden hue, enticing you with their aromatic appeal.
Step 8: Cool Before Serving
Once baked, remove the muffins from the oven and allow them to cool in the pan for about 10 minutes. Then, transfer them to a wire rack to cool completely. For best results, store them in an airtight container for up to three days, allowing the flavors to meld beautifully.

What to Serve with Keto Pumpkin Cream Cheese Muffins
Enjoy the rich flavors of fall with delightful pairings that elevate your muffin experience!
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Warm Spiced Apple Cider: Enhances the autumn vibe with its sweet, spiced notes and tangy apple flavors that resonate beautifully with the muffins.
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Crispy Bacon Strips: Add a savory touch with crispy bacon, offering a delightful contrast to the sweet, creamy muffins while keeping your meal keto-friendly.
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Rich Greek Yogurt: Top your muffins with a dollop of thick Greek yogurt, adding creaminess and a protein boost that perfectly balances the sweetness.
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Fresh Pumpkin Smoothie: Pair your muffins with a refreshing pumpkin smoothie for a comforting, seasonal breakfast—spinach, banana, and almond milk blend well for a nutritious kick.
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Chai Tea Latte: A warm chai latte brings aromatic spices to the table, enhancing the warm flavors of your muffins while providing a cozy beverage option.
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Nutty Trail Mix: Create a crunchy side of nutty trail mix, featuring almonds and pecans for a satisfying texture and taste combo that complements the softness of the muffins beautifully.
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Dark Chocolate Squares: If you’re craving something sweet, enjoy a piece of dark chocolate alongside your muffin for a deliciously rich finish that remains keto-compliant.
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Creamy Avocado Toast: Combine your muffins with a slice of avocado toast for a delightful mix of flavors and textures, adding healthy fats to your meal.
Variations & Substitutions for Keto Pumpkin Cheesecake Muffins
Feel free to get creative with these muffins and make them your own—there’s a world of deliciousness waiting to be explored!
- Nutty Add-In: Add chopped pecans or walnuts for a delightful crunch in each bite.
- Dairy-Free Option: Substitute the cream cheese with a vegan cream cheese alternative for a dairy-free twist.
- Coconut Flour Swap: If desired, use coconut flour in place of almond flour; just remember to adjust the quantity as coconut flour absorbs more moisture.
- Spice It Up: Try using a mix of cinnamon, nutmeg, and ginger instead of pumpkin pie spice for a unique flavor variation that’s just as delightful.
- Chocolate Bliss: Add sugar-free chocolate chips to the batter for a sweet surprise in every muffin—just be mindful of the added carbs.
- Increased Sweetness: If you prefer sweeter muffins, boost the erythritol a little or consider a mix of sweeteners for a more tailored taste.
- Extra Creaminess: For an extra creamy texture, swirl in some Greek yogurt or sour cream along with the cream cheese filling.
- Zesty Touch: Add a teaspoon of orange or lemon zest to brighten and enhance the flavors of the pumpkin.
Each variation allows you to tailor these wonderful Keto Pumpkin Cheesecake Muffins to your taste! If you’re looking for more keto-friendly meal ideas, try my refreshing Keto Avocado Shrimp or a flavorful Keto Cobb Egg salad for a delightful twist!
Make Ahead Options
These Keto Pumpkin Cream Cheese Muffins are ideal for meal prep, making busy mornings a breeze! You can prepare the muffin batter up to 24 hours in advance by mixing the ingredients and storing it in the refrigerator (make sure to cover it tightly to maintain freshness). Additionally, the cream cheese filling can be made ahead of time and kept in the fridge for up to 3 days. When you’re ready to bake, simply scoop the chilled batter into the muffin tins and add the filling. Bake as directed, and you’ll have delightful, fluffy muffins just like fresh-baked in no time! Enjoy the convenience of homemade goodness without the rush!
Expert Tips for Keto Pumpkin Cheesecake Muffins
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Cool Completely: Allow the muffins to cool fully before serving. This helps the cream cheese filling set perfectly and enhances the overall texture.
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Don’t Overmix: When combining dry ingredients, stir gently until just combined. Overmixing can lead to dense muffins, while you want them light and fluffy.
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Room Temperature Ingredients: Ensure your butter and cream cheese are at room temperature. This allows for smoother mixing and prevents lumps in the batter for your Keto muffins.
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Check for Freshness: Always verify that your baking soda is fresh. Stale baking soda can affect the rise of your muffins, leading to flat treats instead of delightful puffs.
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Flavor Twists: Feel free to add your favorite nuts or a sprinkle of chocolate chips to the batter for a fun variation. Keep in mind, however, that this might slightly alter the carb count.
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Storage Tips: Store your Keto Pumpkin Cheesecake Muffins in an airtight container in the fridge for up to 3 days, or freeze for longer freshness. They thaw beautifully!
Storage Tips for Keto Pumpkin Cheesecake Muffins
Fridge: Store your muffins in an airtight container in the fridge for up to 3 days to maintain freshness and flavor.
Freezer: For longer storage, individually wrap the muffins in plastic wrap and then in foil before placing them in the freezer. They can last for up to 2 months.
Thawing: To enjoy your frozen Keto Pumpkin Cheesecake Muffins, simply unwrap and leave them at room temperature for a couple of hours or microwave for a quick warm-up.
Reheating: Use a microwave for 10-15 seconds to reheat. This helps restore their soft texture and creamy filling, making them delightful again!

Keto Pumpkin Cheesecake Muffins Recipe FAQs
What type of pumpkin puree should I use?
Absolutely! For the best results, always opt for pure pumpkin puree with no additives. Avoid pumpkin pie filling as it contains sugars and spices that will alter the flavor and carb count.
How should I store Keto Pumpkin Cheesecake Muffins?
You can store your muffins in an airtight container in the fridge for up to 3 days. This helps maintain their moisture and freshness. Just make sure they cool completely before storing to prevent condensation.
Can I freeze these muffins?
Very! To freeze your Keto Pumpkin Cheesecake Muffins, wrap each muffin individually in plastic wrap, then wrap them in foil to prevent freezer burn. They can be frozen for up to 2 months. When ready to eat, thaw them at room temperature for a couple of hours or microwave them for about 10-15 seconds for a fresh-out-of-the-oven taste.
What if my muffins came out too dense?
If your muffins turned out dense, it may be from overmixing the batter or using too much almond flour. Remember to stir the dry ingredients gently until just combined. Always ensure your baking soda is fresh as well; stale baking soda can result in poor rising.
Are these muffins safe for pets?
No, these muffins are not safe for pets, particularly because they contain xylitol and other sweeteners that can be harmful to dogs. Always keep them out of reach and stick with treats specially formulated for your furry friends.
Can I make adjustments for allergies?
Absolutely! If you have nut allergies, consider substituting almond flour with a seed-based flour like sunflower seed flour. Just note that this may change the flavor and texture somewhat, so check for adjustments in baking time and moisture.

Keto Pumpkin Cheesecake Muffins: Your New Favorite Snack
Ingredients
Equipment
Method
- Preheat your oven to 350°F (175°C). Grease a 12-count muffin pan or line it with parchment paper.
- In a small mixing bowl, combine cream cheese, powdered erythritol, and vanilla extract. Beat until smooth.
- In a large mixing bowl, cream together the butter and Swerve until light and fluffy. Gradually add in eggs, pumpkin puree, and vanilla, mixing well.
- Add almond flour, pumpkin pie spice, baking soda, and salt. Stir gently until just combined.
- Divide the muffin batter into prepared muffin cups, filling about two-thirds full. Add a tablespoon of cream cheese filling on top of each.
- Gently swirl the cream cheese filling into the muffin batter using a fork.
- Bake for about 25 minutes or until a toothpick comes out clean. The tops should be golden.
- Allow muffins to cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.







