When the air turns crisp and leaves start to paint the world in shades of gold and red, pumpkin recipes begin to make their way into our kitchens. From pumpkin pies to lattes, there’s something about this seasonal flavor that captures the warmth and comfort of autumn. Among the best fall bakes you can make at home are Pumpkin Cream Cheese Swirl Muffins – soft, moist pumpkin spice muffins with a luscious cream cheese swirl baked right inside.

These muffins are the perfect fusion of spiced pumpkin goodness and cheesecake-like richness. They’re ideal for cozy breakfasts, Thanksgiving brunch spreads, or as a sweet snack with a hot cup of coffee or tea. Not only do they look bakery-worthy, but they’re also surprisingly easy to make.

In this guide, we’ll cover the recipe step by step, share baking tips, and suggest creative serving ideas that will make these muffins a seasonal favorite in your household.

Ingredients

1 ¾ cups all-purpose flour
1 cup pumpkin puree (not pumpkin pie filling)
1 cup granulated sugar
½ cup brown sugar
½ cup vegetable oil (or melted butter)
2 large eggs
¼ cup milk
1 tsp vanilla extract
1 tsp baking soda
1 tsp baking powder
½ tsp salt
2 tsp ground cinnamon
1 tsp ground pumpkin pie spice (or nutmeg, cloves, and ginger mix)

For Cream Cheese Swirl:

8 oz cream cheese, softened
¼ cup granulated sugar
1 egg yolk
½ tsp vanilla extract

Instructions

Preheat Oven
Preheat oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners.
Make Muffin Batter
In a large bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, and pumpkin pie spice. In another bowl, whisk pumpkin puree, granulated sugar, brown sugar, oil, eggs, milk, and vanilla until smooth. Slowly add the dry ingredients into the wet mixture and stir until just combined.
Prepare Cream Cheese Filling
In a medium bowl, beat cream cheese, sugar, egg yolk, and vanilla until smooth and creamy.
Assemble Muffins
Fill each muffin liner about two-thirds full with pumpkin batter. Drop 1 tablespoon of the cream cheese mixture on top of each muffin, then use a toothpick or skewer to gently swirl it into the batter for a marbled effect.
Bake Muffins
Bake for 18–22 minutes, or until a toothpick inserted into the muffin (away from the cream cheese center) comes out clean.
Cool & Serve
Allow muffins to cool in the pan for 5 minutes before transferring them to a wire rack. Serve warm or at room temperature.

Why You’ll Love These Muffins

Moist Texture: Thanks to pumpkin puree and oil.
Perfect Swirl: The cream cheese filling looks stunning and tastes like cheesecake in a muffin.
Warm Spices: Cinnamon and pumpkin pie spice create that signature autumn flavor.
Make-Ahead Friendly: They stay fresh for days and can be frozen.

Baking Tips & Variations

Don’t Overmix: Mix batter just until the dry ingredients are incorporated for fluffy muffins.
Add Crunch: Top with chopped pecans or walnuts before baking.
Healthier Option: Swap half the flour with whole wheat flour and reduce sugar slightly.
Mini Muffins: Use a mini muffin pan and bake for 12–14 minutes for bite-sized treats.
Frost Option: Drizzle with a cream cheese glaze for extra indulgence.