Pumpkin Cream Cheese Muffins

Section: Fun Meals Kids Will Love

These moist pumpkin muffins are layered with a rich, creamy cheese filling and topped with crunchy pumpkin seeds and raw sugar for texture. The blend of warm spices like cinnamon, nutmeg, ginger, and cloves adds depth, complementing the natural sweetness of pumpkin purée. Made with a balance of brown and granulated sugars, melted butter, and a splash of milk, the batter creates soft, tender muffins with a slightly crisp top. Baking until golden and cooled properly ensures perfect texture and taste.

Harper
Contributed by Harper
Last updated on Tue, 21 Oct 2025 18:42:19 GMT
Pumpkin Cream Cheese Muffins with a white frosting. Save
Pumpkin Cream Cheese Muffins with a white frosting. | flavorrhaven.com

These pumpkin cream cheese muffins bring together the perfect balance of spiced pumpkin flavor and creamy indulgence. I have recreated this Starbucks favorite to enjoy at home, and they have quickly become a go-to fall treat for my family and friends. The muffins are moist, tender, and filled with a luscious cream cheese center that makes every bite feel special.

I remember making these for my kids’ autumn school events and receiving countless requests to bring them again. These muffins hold up beautifully and taste as good the next day, which makes them perfect for sharing.

Ingredients

  • Cream Cheese Filling: 6 ounces cream cheese softened to room temperature for smooth mixing
  • 3 tablespoons granulated sugar for sweetness
  • Half teaspoon vanilla extract to enhance flavor depth
  • Pumpkin Muffins: One and three-quarters cups all-purpose flour provides structure& use a good quality unbleached flour if possible
  • 1 teaspoon baking soda for leavening
  • Half teaspoon baking powder to help muffins rise and stay tender
  • Half teaspoon salt to balance sweetness
  • 2 teaspoons cinnamon for warm spice flavor
  • Half teaspoon ground nutmeg adds complexity and warmth
  • Quarter teaspoon ground ginger for a gentle kick
  • Quarter teaspoon ground cloves brings earthiness and depth
  • Three quarters cup canned pumpkin purée for moistness and natural sweetness& choose pure pumpkin instead of pie filling
  • Three quarters cup granulated sugar for sweetness
  • Half cup light brown sugar packed for rich caramel notes
  • Quarter cup vegetable oil to keep muffins moist
  • Quarter cup unsalted butter melted and slightly cooled for richness
  • Quarter cup milk for tender crumb& whole milk works best
  • 2 large eggs for binding and moisture
  • 1 teaspoon vanilla extract to enhance all flavors
  • Topping: 2 tablespoons raw sugar adds crunch on top
  • 2 tablespoons pumpkin seeds for nutty texture and presentation

Instructions

Spoon the Cream Cheese Filling:
Whip softened cream cheese, granulated sugar, and vanilla extract in a small bowl with a hand mixer until smooth and creamy. Transfer to a piping bag or ziplock bag, seal, and chill in the refrigerator for 30 minutes.
Mix the Dry Ingredients:
Preheat oven to 350 degrees Fahrenheit (177 degrees Celsius) and line a 12-cup muffin pan with liners. In a medium bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, nutmeg, ginger, and cloves to evenly distribute the spices and leavening agents.
Blend the Wet Ingredients:
In a large bowl, beat pumpkin purée, granulated sugar, brown sugar, vegetable oil, melted butter, milk, eggs, and vanilla extract with a hand mixer until the mixture is smooth and homogenous.
Combine Dry and Wet Mixtures:
Pour the flour mixture into the wet ingredients and fold gently using a spatula just until combined. Be careful not to overmix to keep the muffins tender.
Fill Muffin Tins and Add Filling:
Divide batter evenly into prepared liners, filling each about three quarters full. Pipe about one tablespoon of the chilled cream cheese filling into the center of each muffin batter mound. This creates a delicious surprise inside.
Add Toppings and Bake:
Sprinkle raw sugar and pumpkin seeds over the tops of the muffins for texture and a pretty finish. Bake for 18 to 22 minutes until the muffin tops are set and a toothpick inserted into the pumpkin portion comes out clean.
Cool Before Serving:
Allow muffins to cool in the pan for 10 minutes before transferring to a wire rack to cool completely. This prevents the cream cheese center from leaking and helps muffins firm up.
Pumpkin Cream Cheese Muffins.
Pumpkin Cream Cheese Muffins. | flavorrhaven.com

The pumpkin purée is my favorite ingredient here& its natural sweetness combined with the spices creates a flavor that instantly reminds me of crisp autumn mornings. Baking and sharing these with my family always adds a little extra warmth to the season.

Storage Tips

Store these muffins in an airtight container at room temperature for up to two days. For longer storage, wrap each muffin individually with plastic wrap and freeze in a resealable freezer bag for up to three months. Thaw overnight in the refrigerator or warm briefly in the microwave before serving.

Ingredient Substitutions

Use Greek yogurt in place of some or all of the oil for a lighter texture but be careful to not add extra moisture that might affect the cream cheese center. Ground allspice can substitute for the combination of cloves, nutmeg, and ginger if you want to simplify the spice mix. Almond milk or oat milk work well instead of cow’s milk if you prefer a dairy-free version.

Serving Suggestions

These muffins make a perfect breakfast or afternoon snack paired with a cup of coffee or spiced tea. They also work well as an elegant dessert when served slightly warmed with a drizzle of maple syrup or a dusting of powdered sugar.

A plate of pumpkin cream cheese muffins.
A plate of pumpkin cream cheese muffins. | flavorrhaven.com

I learned the hard way not to skip chilling the cream cheese filling since warm filling can melt too much into the batter and lose its signature center.

FAQs about Recipes

→ How do I achieve a creamy filling inside the muffins?

Beat softened cream cheese with sugar and vanilla until smooth, then chill before piping into muffin centers.

→ What spices enhance the pumpkin flavor here?

A warm mixture of cinnamon, nutmeg, ginger, and cloves perfectly complements the pumpkin’s natural sweetness.

→ Can I substitute the oil with another fat?

You can replace vegetable oil with melted butter for a richer flavor and texture in the muffins.

→ How to know when the muffins are baked thoroughly?

Check by inserting a toothpick into the pumpkin part; it should come out clean when done baking.

→ What is the purpose of pumpkin seeds on top?

They add a delightful crunch and a nutty contrast to the soft, spiced muffin texture.

Pumpkin Cream Cheese Muffins

Moist pumpkin spiced muffins filled with creamy cheese and topped with pumpkin seeds and sugar.

Prep Time
20 mins
Cooking Time
22 mins
Overall Time
42 mins
Contributed by: Harper

Recipe Category: Kid-Friendly

Skill Level: Moderate

Cuisine Type: American

Recipe Output: 12 Portion Size (12 muffins)

Dietary Features: Vegetarian-Friendly

What You'll Need

→ Cream Cheese Filling

01 6 oz cream cheese, softened
02 3 tablespoons granulated sugar
03 ½ teaspoon vanilla extract

→ Pumpkin Muffins

04 1 ¾ cups all-purpose flour
05 1 teaspoon baking soda
06 ½ teaspoon baking powder
07 ½ teaspoon salt
08 2 teaspoons ground cinnamon
09 ½ teaspoon ground nutmeg
10 ¼ teaspoon ground ginger
11 ¼ teaspoon ground cloves
12 ¾ cup canned pumpkin purée
13 ¾ cup granulated sugar
14 ½ cup packed light brown sugar
15 ¼ cup vegetable oil
16 ¼ cup unsalted butter, melted and slightly cooled
17 ¼ cup milk
18 2 large eggs
19 1 teaspoon vanilla extract

→ Topping

20 2 tablespoons raw sugar
21 2 tablespoons pumpkin seeds

Step-by-Step Guide

Step 01

In a small bowl, beat the softened cream cheese, granulated sugar, and vanilla extract with a hand mixer until smooth and creamy. Transfer the mixture to a piping bag or ziplock bag and refrigerate for 30 minutes.

Step 02

Preheat the oven to 350°F. Line a 12-cup muffin pan with cupcake liners.

Step 03

In a medium bowl, whisk together all-purpose flour, baking soda, baking powder, salt, cinnamon, nutmeg, ginger, and cloves until evenly distributed.

Step 04

In a large bowl, combine canned pumpkin purée, granulated sugar, light brown sugar, vegetable oil, melted butter, milk, eggs, and vanilla extract. Beat with a hand mixer until smooth and homogenous.

Step 05

Gently fold the dry ingredient mixture into the wet ingredients until just combined, avoiding overmixing to maintain a tender crumb.

Step 06

Spoon the batter evenly into the prepared liners, filling each about ¾ full. Pipe approximately 1 tablespoon of chilled cream cheese filling into the center of each muffin.

Step 07

Sprinkle each muffin with raw sugar and pumpkin seeds. Bake in the preheated oven for 18 to 22 minutes, or until muffin tops are set and a toothpick inserted into the pumpkin portion comes out clean.

Step 08

Allow muffins to cool in the pan for 10 minutes before transferring to a wire rack to cool completely.

Additional Notes

  1. Chilling the cream cheese filling helps maintain its shape when piping into the batter.

Tools You'll Need

  • 12-cup muffin pan
  • Cupcake liners
  • Hand mixer
  • Mixing bowls
  • Piping bag or ziplock bag
  • Wire cooling rack

Allergen Notices

Inspect every ingredient for potential allergens and seek expert advice if necessary.
  • Contains dairy, eggs, gluten

Per Serving Nutritional Info

Keep in mind these are general guidelines, not a replacement for professional advice.
  • Calories: 320
  • Fats: 14 grams
  • Carbohydrates: 45 grams
  • Proteins: 5 grams