Starbucks Pumpkin Cream Cheese Muffins

I still remember the first time I walked into Starbucks during pumpkin season and spotted those cream cheese muffins in the case. They looked so rich, golden, and inviting that I had to try one.

The flavor lived up to the look: soft pumpkin cake, warm spices, and that creamy cheesecake-style center that made every bite feel indulgent.

The only downside was how heavy they were on sugar and carbs, which made me feel guilty after enjoying them. That’s when I started testing my own recipe at home.

I wanted the same taste and texture—the moist pumpkin crumb, the creamy center, the nutty crunch from pumpkin seeds—but without the sugar overload.

After a lot of baking sessions, I landed on this low carb recipe that hits all the notes of the original while being so much lighter.

You still get the rich cream cheese center, the soft pumpkin muffin, and the roasted seeds on top.

The difference is that you can enjoy them more often without worrying about the sugar crash.

These muffins have become a staple in my kitchen. I make a batch, keep a few in the fridge, and freeze the rest so I can grab one any time I want that Starbucks flavor without the trip—or the guilt.

They’re great for breakfast, a mid-afternoon snack, or even dessert. And the best part is, they taste just as good as they look.

Table of Contents

Low Carb Starbucks Pumpkin Cream Cheese Muffins

Ingredients

For The Muffins

1 ½ cups fine almond flour
¼ cup coconut flour
2 teaspoons baking powder
½ teaspoon baking soda
½ teaspoon salt
2 teaspoons ground cinnamon
1 teaspoon ground nutmeg
½ teaspoon ground cloves
½ teaspoon ground ginger
½ cup pumpkin puree (not pumpkin pie filling)
⅔ cup granulated erythritol or monk fruit sweetener
3 large eggs, room temperature
⅓ cup unsweetened almond milk
⅓ cup melted butter or refined coconut oil
1 teaspoon vanilla extract

For The Cream Cheese Filling

6 ounces cream cheese, softened
3 tablespoons powdered erythritol or monk fruit sweetener
½ teaspoon vanilla extract

For The Topping

¼ cup roasted pumpkin seeds (pepitas)
2 tablespoons chopped pecans or walnuts (optional)

Instructions

Preheat oven to 350°F (175°C) and line a 12-cup muffin pan with parchment paper liners or lightly grease the pan.
In a medium bowl, whisk together almond flour, coconut flour, baking powder, baking soda, salt, cinnamon, nutmeg, cloves, and ginger. Set aside.
In a large mixing bowl, combine pumpkin puree, granulated sweetener, eggs, almond milk, melted butter, and vanilla extract. Whisk until smooth and well blended.
Gradually add the dry ingredients into the wet mixture, stirring until a thick batter forms. Do not overmix.
In a separate small bowl, beat softened cream cheese with powdered sweetener and vanilla until creamy and smooth. This will be the filling.
Divide the muffin batter evenly among the prepared muffin cups, filling each about two-thirds full.
Use the back of a spoon or your finger to make a small well in the center of each muffin. Spoon about 1 teaspoon of the cream cheese mixture into each well.
Sprinkle pumpkin seeds and chopped nuts over the tops of the muffins. Gently press them down so they stick.
Bake for 20–24 minutes, or until the muffins are golden brown and a toothpick inserted near the edge (not through the cream cheese center) comes out clean.
Allow muffins to cool in the pan for 10 minutes, then carefully transfer to a wire rack to cool completely. The cream cheese filling will set as they cool.

What Makes These Muffins Low Carb?

These muffins are made with almond flour and coconut flour instead of regular all-purpose flour. They are also sweetened with low-carb sweeteners like monk fruit or erythritol rather than sugar.

This makes them much lower in carbs while still tasting soft, moist, and flavorful. By swapping these key ingredients, you get the same warm pumpkin spice taste but without the sugar spike.

Can I Use Canned Pumpkin Or Fresh Pumpkin Puree?

Both options can work, but they give slightly different results.

Canned pumpkin puree: This is the easiest and most reliable option. It has a thick consistency, smooth texture, and rich pumpkin flavor. Make sure to use pure pumpkin puree and not pumpkin pie filling.
Homemade fresh puree: You can roast and mash fresh pumpkin, but it often has more water, which can make the batter too thin. If you use homemade puree, drain it in a cheesecloth or sieve to remove excess liquid.

How Do I Make The Cream Cheese Center Smooth?

The creamy filling is the highlight of these muffins, so it’s important to prepare it correctly.

Soften the cream cheese: Always start with cream cheese at room temperature, or it will turn lumpy when mixed.
Beat until fluffy: Whip the cream cheese with powdered sweetener and vanilla until smooth and airy.
Spoon carefully: Place the filling gently in the center of each muffin so it bakes into the batter without sinking to the bottom.

Can I Replace Almond Flour With Another Low Carb Flour?

Almond flour gives these muffins a soft and moist texture, but you may want alternatives.

Coconut flour: If you use only coconut flour, the muffins may turn out dry since it absorbs a lot of liquid. Adjust with more eggs and pumpkin puree.
Sunflower seed flour: This works as a nut-free option and can be swapped in equal amounts for almond flour.
Combination flours: A mix of almond and coconut flour gives the best balance of moisture and structure.

How Do I Store Pumpkin Cream Cheese Muffins?

Proper storage keeps the muffins fresh and safe to eat.

At room temperature: Since they contain cream cheese filling, avoid leaving them out for more than 2 hours.
In the fridge: Store cooled muffins in an airtight container for up to 5 days. The cream cheese center stays firm and fresh this way.
In the freezer: Place muffins in a freezer-safe bag or container and freeze for up to 2 months. Thaw them overnight in the fridge or warm slightly in the microwave before eating.

Can I Make These Muffins Ahead Of Time?

Yes, these muffins are perfect for meal prep and busy mornings.

Bake and store: Prepare them fully, cool, and refrigerate. They’ll be ready to grab anytime.
Freeze for later: Keep a batch in the freezer and reheat as needed. They taste just as good after thawing.
Prepare the batter ahead: You can also mix the batter, store it covered in the fridge overnight, and bake fresh the next morning. Just add the cream cheese filling before baking.

What Can I Use Instead Of Pumpkin Seeds On Top?

Pumpkin seeds add a nice crunch and nutty taste, but you can swap them if you prefer.

Chopped pecans or walnuts: These give a toasty crunch and pair well with pumpkin spice.
Sunflower seeds: Great for those who want a nut-free option.
No topping: You can bake them plain if you want a softer muffin without added crunch.

Can These Muffins Be Made Dairy-Free?

Yes, with a few smart swaps you can make them dairy-free while keeping the flavor.

Cream cheese filling: Use dairy-free cream cheese alternatives made from cashews or almonds.
Butter substitute: Replace butter with melted coconut oil or a neutral oil.
Milk substitutes: If a splash of milk is used, almond milk or coconut milk works well.

Do These Muffins Taste Like Starbucks?

They are inspired by Starbucks’ famous pumpkin cream cheese muffins but made low carb. The flavor is very close: spiced pumpkin base, creamy sweet center, and crunchy seeds on top.

The main difference is that they are lighter, less sweet, and won’t leave you feeling heavy. Many people find them just as satisfying, if not better, because they don’t cause a sugar crash afterward.