Pumpkin Cheesecake Muffins

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By: Ashley Wilson | Published: August 13, 2025 | Updated: November 26, 2025

Pumpkin cheesecake muffin with creamy cheesecake swirl on rustic plate

If you love pumpkin muffins and cream cheese desserts, these pumpkin cheesecake muffins will be your new fall favorite. Imagine the rich, spiced flavor of classic pumpkin muffins combined with a sweet, tangy cheesecake center—perfect for breakfast, dessert, or an afternoon coffee break. Whether you’re a fan of Starbucks pumpkin cream cheese muffins or traditional pumpkin cream cheese muffins, this easy recipe delivers bakery-quality results right in your kitchen.

Why You’ll Love This Recipe

  • Moist and flavorful thanks to pumpkin puree and warm spices.
  • Creamy cheesecake filling makes them extra indulgent.
  • Inspired by the coffee shop classic but budget-friendly.
  • Perfect for fall gatherings, holiday breakfasts, or gifting.

Ingredients

Flat lay of pumpkin cheesecake muffin ingredients including pumpkin puree, cream cheese, and spices
Pumpkin Cheesecake Muffins 12

For the Muffins:

  • 1 ¾ cups all-purpose flour
  • 1 teaspoon baking soda
  • 2 teaspoons pumpkin pie spice
  • ½ teaspoon salt
  • 1 cup pumpkin puree
  • ½ cup vegetable oil
  • ½ cup granulated sugar
  • ½ cup brown sugar, packed
  • 2 large eggs
  • 1 teaspoon vanilla extract

For the Cheesecake Filling:

  • 8 oz cream cheese, softened
  • ¼ cup granulated sugar
  • 1 teaspoon vanilla extract

Optional Topping:

  • ¼ cup pumpkin seeds (pepitas)

Step-by-Step Instructions

Collage showing mixing batter, adding cream cheese filling, and baked muffins
Pumpkin Cheesecake Muffins 13
  • Step 1 – Preheat & Prep
  • Preheat oven to 350°F (175°C). Line a muffin tin with paper liners.
  • Step 2 – Mix Dry Ingredients
  • In a medium bowl, whisk flour, baking soda, pumpkin pie spice, and salt.
  • Step 3 – Combine Wet Ingredients
  • In a large bowl, whisk pumpkin puree, oil, sugars, eggs, and vanilla until smooth.
  • Step 4 – Make Cheesecake Filling
  • Beat cream cheese, sugar, and vanilla together until creamy.
  • Step 5 – Assemble Muffins
  • Fill muffin cups halfway with pumpkin batter, add a spoonful of cheesecake filling, then top with more pumpkin batter. Swirl gently with a knife. Sprinkle with pumpkin seeds if desired.
  • Step 6 – Bake
  • Bake for 18–22 minutes or until a toothpick inserted in the muffin part comes out clean. Cool for 5 minutes before transferring to a wire rack.

Tips for the Best Pumpkin Cheesecake Muffins

  • Use room-temperature cream cheese for the smoothest filling.
  • Don’t overmix the batter—this keeps the muffins tender.
  • For a Starbucks-style look, keep the cheesecake filling slightly exposed on top.
  • Freeze cooled muffins for up to 2 months.

Serving Suggestions

Plate of pumpkin cheesecake muffins with coffee and autumn decor
Pumpkin Cheesecake Muffins 14

Serve these muffins warm with coffee or tea for the perfect cozy breakfast. They’re also great for brunch spreads, alongside savory bites like sausage cream cheese crescent rolls for a sweet-and-savory balance.

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Pumpkin cheesecake muffin with creamy cheesecake swirl on rustic plate

Pumpkin Cheesecake Muffins


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  • Author: Ashley Wilson
  • Total Time: 35 minutes
  • Yield: 12 muffins 1x
  • Diet: Vegetarian

Description

Moist and spiced pumpkin muffins with a creamy cheesecake center, inspired by the coffee shop classic. These bakery-style treats are perfect for fall breakfasts, holiday gatherings, or as a cozy afternoon snack.


Ingredients

Scale

For the Muffins:

1 ¾ cups all-purpose flour

1 teaspoon baking soda

2 teaspoons pumpkin pie spice

½ teaspoon salt

1 cup pumpkin puree

½ cup vegetable oil

½ cup granulated sugar

½ cup brown sugar, packed

2 large eggs

1 teaspoon vanilla extract

For the Cheesecake Filling:

8 oz cream cheese, softened

¼ cup granulated sugar

1 teaspoon vanilla extract

Optional Topping:

¼ cup pumpkin seeds (pepitas)


Instructions

1. Preheat oven to 350°F (175°C). Line a muffin tin with paper liners.

2. In a medium bowl, whisk flour, baking soda, pumpkin pie spice, and salt.

3. In a large bowl, whisk pumpkin puree, oil, granulated sugar, brown sugar, eggs, and vanilla until smooth.

4. Beat cream cheese, sugar, and vanilla together until creamy.

5. Fill muffin cups halfway with pumpkin batter, add a spoonful of cheesecake filling, then top with more pumpkin batter. Swirl gently with a knife. Sprinkle with pumpkin seeds if desired.

6. Bake for 18–22 minutes or until a toothpick inserted in the muffin part comes out clean. Cool for 5 minutes before transferring to a wire rack.

Notes

Use room-temperature cream cheese for the smoothest filling.

Don’t overmix the batter to keep muffins tender.

For a Starbucks-style look, keep some cheesecake filling slightly exposed on top.

Freeze cooled muffins for up to 2 months.

  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Category: Breakfast, Dessert, Snack
  • Method: Baking
  • Cuisine: American

Nutrition

  • Serving Size: 1 muffin
  • Calories: 280
  • Sugar: 22g
  • Sodium: 190mg
  • Fat: 14g
  • Saturated Fat: 5g
  • Unsaturated Fat: 8g
  • Trans Fat: 0g
  • Carbohydrates: 34g
  • Fiber: 2g
  • Protein: 4g
  • Cholesterol: 45mg

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