Keto Pumpkin Cream Cheese Swirl Muffins Recipe

Enjoy fluffy, flavorful keto pumpkin cream cheese muffins with a beautiful cream cheese swirl. These moist muffins make a cozy fall treat without added sugar and with only 5 grams net carbs per muffin.

Keto Pumpkin Muffins

Pumpkin rolls and pumpkin bread are classic autumn desserts. This recipe turns those flavors into light, tender keto pumpkin muffins with a surprise cream cheese swirl in each one. They’re ideal for breakfast, snacks, or gatherings and are quick to make ahead.

With only 5 grams net carbs per muffin, these fit easily into a low-carb or keto lifestyle while still tasting indulgent.

Keto Pumpkin Cream Cheese Muffins

Muffins are perfect for meal prep—make a batch for the week, bring them to a party, or pack them in lunch boxes. These pumpkin muffins are sugar-free, naturally gluten-free, and rich in healthy fats from almond flour and butter, giving them great texture and flavor.

The muffins contain no added sugar and rely on a sugar substitute for sweetness. The cream cheese swirl adds a creamy contrast to the spiced pumpkin batter.

Pumpkin Cream Cheese Swirl Muffins

Although pumpkin puree has some carbs, this recipe uses just 2/3 cup for the entire batch, which helps keep the net carbs low. For convenience, use a jarred pumpkin pie spice; if you don’t have it, make a blend from cinnamon, cloves, allspice, and nutmeg. Apple pie spice can be used as a substitute—add a pinch of ground cloves if you want it closer to pumpkin pie spice.

Gluten-Free Pumpkin Muffins

This recipe uses blanched almond flour instead of all-purpose flour. Almond flour creates a moist crumb and keeps the muffins gluten-free. It’s important to use blanched almond flour rather than almond meal—almond meal includes the nut skins and gives a grainier texture, while blanched almond flour is finer and better for baking.

How to Freeze Muffins

Freezing these muffins is simple and convenient. Properly stored, they keep up to six months—great for making a big batch ahead of the season. After baking and cooling to room temperature, wrap each muffin individually in plastic wrap, then place them in a large freezer-safe resealable bag. Wrapping them first prevents the muffins from freezing together into one big mass.

Keto Pumpkin Cream Cheese Muffins Recipe

Below is the recipe overview. Exact measurements and step-by-step instructions are included in the printable recipe card in the recipe section.

Prep Time: 20 minutes
Cook Time: 25 minutes
Servings: 9 muffins
Net Carbs: 5 net carbs per muffin

Ingredients:

Almond flour
Large eggs
Butter, softened
Vanilla extract
Pumpkin puree (2/3 cup)
Baking powder
Baking soda
Pumpkin pie spice
Swerve confectioners sugar substitute (or similar)
Cream cheese, softened

Instructions:

Preheat the oven to 350°F and line a 9-cup muffin tin with liners.

In a mixing bowl, combine the almond flour, eggs, softened butter, vanilla, pumpkin puree, baking powder, baking soda, pumpkin pie spice, and 1/2 cup of the Swerve. Mix until smooth and well combined.

Fill each liner about two-thirds full with batter.

In a separate bowl, beat the softened cream cheese with 3 tablespoons of Swerve until smooth.

Spoon a dollop of the cream cheese mixture onto each muffin and use the tip of a knife to gently swirl it into the pumpkin batter.

Bake for about 25 minutes, until a toothpick inserted into the muffin (avoiding the cream cheese swirl) comes out clean. Allow to cool before serving.

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Keto Muffins

If you like these pumpkin cream cheese muffins, try other keto muffin recipes for variety. They’re great for breakfast or a satisfying snack.

• Keto Brownie Muffins
• Keto Blueberry Muffins
• Low-Carb Cheddar Jalapeno Muffins
• Keto Sausage Muffins