Pumpkin Cream Cheese Muffins

5 from 6 votes
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Make a batch of pumpkin cream cheese muffins for a quick, easy, fall-inspired breakfast. Each handheld treat contains fresh pumpkin, bold spices, a creamy filling, and crunchy praline pepitas.

Pumpkin cream cheese muffins recipe inspired by Starbucks own recipe.

When the fall season arrives, so do many enticing pumpkin-flavored treats. In particular, the pumpkin cream cheese muffins at Starbucks always catch my eye as I’m ordering a pumpkin spice latte. Just like the drink, here is my homemade version of the muffins so that you can bake a big batch for the family to enjoy throughout the week.

A tender pumpkin spice cake is ideal for adding a velvety cream cheese mixture and some candied pumpkin seeds. The freshly baked muffins rival coffee shop versions and will save you money by making them at home. Win, win!

A pan of pepitas cooking in butter and sugar.

Make the pumpkin seed pralines

The tops of the muffins are sprinkled with crunchy, candied pumpkin seeds. This adds extra texture to the surface. It’s delicious! I use pepitas, which are hulled pumpkin seeds that are green in color. To candy them, they cook over medium heat in melted butter and granulated sugar. Once the mixture turns a light golden brown hue and looks glossy, a caramel flavor will emerge in just a few minutes.

This process happens between 320 to 350ºF (160 to 177ºC). Don’t let it get too hot, or it will burn! Cool the candied seed mixture in a single layer on the parchment paper-lined sheet tray. In about 10 minutes, the sugar coating will harden. You can roughly chop it up or sprinkle them whole on the muffins. If you want to skip this step, instead, add the plain pumpkin seeds.

Pumpkin selection

Pumpkin puree is added as the base ingredient, adding a creamy, slightly sweet taste of winter squash. For convenience, use canned pumpkin, also labeled as 100% pumpkin. You could also make pumpkin puree from scratch and roast pumpkin seeds for a healthy snack.

Skip the canned pumpkin pie filling. It is already sweetened with spices added. It will make the muffins too sugary.

Make the pumpkin muffin batter

I used my trusty pumpkin muffin recipe as the base. It’s brimming with flavor, brown sugar for a hint of molasses, and plenty of pumpkin pie spice. When baked, the aromas of cinnamon, nutmeg, cloves, ginger, and allspice fill your home.

A combination of baking powder and baking soda guarantees soft muffins with the sought-after domed top. The dry ingredients mix with pumpkin puree, eggs, sour cream, sugars, and vegetable oil. The bright orange batter is ready to be filled.

Pumpkin cupcake batter in a large bowl.

Make the cream cheese frosting

When taking a bite into the muffin, getting a part of the tangy cream cheese frosting in the middle of the cake is a delicious combination. The filling is a simple combination of softened brick cream cheese, sugar, milk, vanilla extract, and cornstarch.

The starch creates a thicker consistency when baked. All-purpose flour is a good swap if you don’t have cornstarch. Like the Starbucks version, I add about 2 teaspoons of filling per muffin. If you enjoy more cream cheese in the center, double the recipe and the amount added.

Whisking homemade cream cheese frosting in a bowl.

How to make pumpkin cream cheese muffins

When the pumpkin muffin batter, cream cheese filling, and praline pumpkin seeds are ready, it’s time to assemble. Use a 12-portion muffin pan, then line it with a muffin cup. I like to double up on the paper liners. Add about ⅓ cup of batter per cup. Use a piping bag to add about 2 teaspoons of filling to the top and center of each muffin.

Sprinkle pumpkin seeds on top of the batter. Don’t place them too close to the edge, as they can burn as the muffins rise and come in contact with the pan. Bake at 350ºF (177ºC) until a toothpick inserted into the middle comes out clean, about 20 minutes. I only let the muffins sit in the pan for 5 minutes, then transfer them to a cooling rack so that they don’t get dried out due to the residual heat.

Serve them with

Frequently asked questions

Is canned pumpkin and pumpkin puree the same thing?

Yes, they are the same ingredient. Pumpkin puree is made with no added seasoning, just 100% of the cooked and pureed squash that’s been canned. Different brands use different pumpkin varieties, so the taste and color may vary slightly.

Can I use pumpkin pie filling instead of pumpkin puree?

No! The filling is pumpkin puree that has already been sweetened with sugar and has added spices like cinnamon, nutmeg, ginger, and cloves. It’s meant to be mixed with eggs and evaporated milk as a shortcut filling for pumpkin pie. Use 100% pumpkin for making muffins and cakes to control the seasoning levels.

Do I have to candy the pumpkin seeds?

Candied pumpkin seeds add a caramelized flavor to the surface and extra crunch to the muffins. You can omit the candying step and sprinkle plain pepitas on top of the muffins.

Pumpkin cream cheese muffin with a bite taken out of it.

Recipe Science

Checking for doneness of pumpkin muffins

Typically cakes are done baking when they reach about 210ºF (99ºC. However, there will be carryover cooking once removed from the oven. Muffins are mini cakes and can dry out easily. A toothpick is a good way for a visual check, no crumbs should be attached. Use a thermometer for more accurate measurement. The cake should reach between 200 to 205ºF (93 to 96ºC), and the residual heat will gently complete the cooking of the batter.

Pumpkin Cream Cheese Muffins

Make fall-inspired pumpkin cream cheese muffins for an easy grab-and-go breakfast. Each handheld treat contains fresh pumpkin, bold spices, a creamy filling, and crunchy seeds.
5 from 6 votes
Prep Time35 minutes
Cook Time25 minutes
Total Time1 hour
Servings 12 muffins
Course Breakfast
Cuisine American


Praline Pumpkin Seeds

  • 2 teaspoons unsalted butter
  • ¼ cup pumpkin seeds, or pepitas
  • 1 tablespoon granulated sugar
  • teaspoon pumpkin pie spice, optional

Pumpkin Muffins

  • 1 ⅔ cups all-purpose flour
  • 1 teaspoon baking soda
  • ½ teaspoon baking powder
  • 3 ¼ teaspoons pumpkin pie spice
  • ½ teaspoon kosher salt
  • 2 large eggs, room temperature
  • 1 cup granulated sugar
  • ¼ cup dark brown sugar, firmly packed
  • ½  cup vegetable oil
  • 1 cup canned pumpkin
  • ¼ cup whole milk
  • ¼  cup sour cream
  • 1 teaspoon pure vanilla extract

Cream Cheese Filling

  • 4 ounces cream cheese, softened
  • 2 tablespoons granulated sugar
  • ½ teaspoon cornstarch
  • 1 teaspoon whole milk
  • ½ teaspoon vanilla extract


  • Heat Oven Set the oven rack to the center position. Preheat to 350ºF (177ºC).
  • Make Praline Topping In a small skillet, melt butter over medium heat. Immediately add the pumpkin seeds and granulated sugar. Cook, constantly stirring, until the sugar is lightly caramelized and glossy, about 2 to 3 minutes. Reduce the heat if browning too quickly. Turn off the heat and stir in the pumpkin pie spice (if using).
    Transfer to a parchment paper-lined sheet pan and spread into a single layer. Cool entirely until hardened, about 10 minutes. If desired, roughly chop for the topping.
  • Prepare Muffin Tin In a 12-cup muffin pan, add paper liners or grease with cooking spray or vegetable oil.
  • Combine Dry Ingredients In a large bowl, sift together the flour, baking soda, baking powder, salt, and pumpkin pie spice. Whisk until combined.
  • Combine Wet Ingredients In a medium bowl, whisk together eggs, granulated sugar, and brown sugar until smooth and pale yellow in color, 1 minute. Slowly whisk in the vegetable oil into the egg mixture until completely mixed, about 30 seconds. Whisk in pumpkin, whole milk, sour cream, and vanilla extract into the egg mixture until smooth, about 30 seconds.
  • Make the Batter – Add the egg mixture to the flour mixture. Gently fold the flour mixture until just moistened, making sure to scrape the bottom with some lumps and flour spots remaining. Do not over-mix the batter.
  • Portion the Muffins Evenly divide the muffin batter amongst the cups, about ⅓ cup per muffin.
  • Make Cream Cheese Filling – In a medium bow,l whisk together the softened cream cheese, sugar, cornstarch, milk, and vanilla extract. Transfer to a piping bag. Add 2 teaspoons of filling in the center of each muffin. Alternatively, use a spoon to add the filling. Sprinkle the praline pumpkin seeds on top of the muffin batter, leaving space along the edges.
  • Bake Bake until a toothpick inserted on the edges comes out clean or the internal temperature reaches 200 to 205°F (93 to 96ºC), about 20 to 22 minutes. Cool the pumpkin muffins in a pan for 5 minutes. Transfer to a wire rack to cool down.


  • Pumpkin Pie Spice Substitute: Combine 2 teaspoon ground cinnamon, ½ teaspoon ground ginger, ¼ teaspoon ground nutmeg, ¼ teaspoon ground cloves, ¼ teaspoon ground allspice for muffin batter. 
  • More Filling: Double the cream cheese filling recipe, adding 4 teaspoons to the center of the muffin instead of 2 teaspoons. 
  • Cornstarch Substitute: Use 1 teaspoon all-purpose flour.  
  • Pumpkin Seed Substitute: Plain chopped pumpkin seeds (or pepitas) can be added to the muffins instead of cooking them in sugar. Sunflower seeds, almond, walnuts, and pecans are delicious swaps, or candied nuts. 
  • Storing: Store in the refrigerator for up to 7 days. Reheat in the microwave on high in 5 to 10-second intervals until warm. 
  • Freezing: Individually wrap each muffin in plastic wrap. Store in a resealable bag in the freezer for up to 1 month. To warm, wrap the muffin in a paper towel and reheat it in the microwave on medium heat for about 60 to 90 seconds. 

Nutrition Facts

Serves: 12 muffins
Calories 233kcal (12%)Carbohydrates 41g (14%)Protein 4g (8%)Fat 6g (9%)Saturated Fat 3g (15%)Polyunsaturated Fat 1gMonounsaturated Fat 2gTrans Fat 0.03gCholesterol 42mg (14%)Sodium 247mg (10%)Potassium 131mg (4%)Fiber 1g (4%)Sugar 26g (29%)Vitamin A 3405IU (68%)Vitamin C 1mg (1%)Calcium 49mg (5%)Iron 1mg (6%)

Percent Daily Values are based on a 2000-calorie diet. All nutritional information is based on estimated third-party calculations. Each recipe and nutritional value will vary depending on the brands you use, measuring methods, and portion sizes per household.

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Jessica Gavin

I'm a culinary school graduate, cookbook author, and a mom who loves croissants! My passion is creating recipes and sharing the science behind cooking to help you gain confidence in the kitchen.

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