If fall had a flavor, it would taste exactly like these Swirled Pumpkin Cream Cheese Muffins. Perfectly spiced, soft, moist pumpkin muffins are topped with a sweet, tangy cream cheese swirl that melts into the batter as they bake — creating the bakery-style pumpkin muffin everyone craves this time of year.

These muffins deliver all the cozy pumpkin spice warmth you want from traditional pumpkin muffins, but the cream cheese swirl adds a velvety, cheesecake-like richness that takes them to the next level. Think pumpkin pie meets cheesecake meets the fluffiest café muffin. And the best part? They’re incredibly easy to make.

No mixers required. No complicated steps. Just whisk, swirl, bake, and enjoy.

Whether you’re baking for a fall breakfast, Thanksgiving brunch, a cozy afternoon treat, or meal prep, these pumpkin cream cheese muffins always impress. They stay moist for days, freeze beautifully, and make your entire house smell like cinnamon, nutmeg, and autumn.

What Makes These Pumpkin Cream Cheese Muffins So Special?

1. The thick, velvety cream cheese swirl

Instead of a dollop hidden inside, the cream cheese is swirled right on top so you get creamy goodness in every bite.

2. Perfect fall spice blend

Pumpkin spice, cinnamon, and vanilla warm the muffins from the inside out.

3. Super moist pumpkin batter

Pumpkin purée keeps these muffins soft for days — no dry muffins here.

4. Better than bakery muffins

Thick tops, soft crumb, and gorgeous swirls that look store-bought but taste way better.

5. Freezer-friendly

Bake once, enjoy for weeks.

Ingredients

Pumpkin Muffin Batter

• 1 3/4 cups all-purpose flour
• 1 cup granulated sugar
• 1/2 cup brown sugar
• 1 tsp baking soda
• 1/2 tsp baking powder
• 1 1/2 tsp pumpkin pie spice
• 1 tsp cinnamon
• 1/2 tsp salt
• 1 cup pumpkin purée
• 2 large eggs
• 1/2 cup vegetable oil
• 1/4 cup milk
• 2 tsp vanilla extract

Cream Cheese Swirl

• 8 oz cream cheese, softened
• 1/4 cup granulated sugar
• 1 tsp vanilla extract
• 1 large egg yolk

Instructions

1. Preheat oven.
   Heat oven to 350°F (175°C). Line a 12-cup muffin pan with liners.
2. Mix dry ingredients.
   In a large bowl, whisk flour, granulated sugar, brown sugar, baking soda, baking powder, pumpkin pie spice, cinnamon, and salt.
3. Mix wet ingredients.
   In another bowl, whisk pumpkin purée, eggs, oil, milk, and vanilla.
4. Combine batter.
   Pour wet ingredients into dry and mix just until combined. Do not overmix.
5. Make cream cheese swirl.
   Beat softened cream cheese, sugar, vanilla, and egg yolk until smooth.
6. Fill muffin tins.
   Divide pumpkin batter evenly among liners (about ¾ full).
7. Add cream cheese swirl.
   Spoon about 1 tablespoon of cream cheese mixture onto each muffin and swirl with a toothpick.
8. Bake.
   Bake 18–22 minutes, or until centers are set and a toothpick comes out clean.
9. Cool.
   Let muffins cool in pan 5 minutes, then transfer to rack.

Swirled Pumpkin Cream Cheese Muffins

Soft, moist pumpkin muffins swirled with tangy cream cheese for the perfect fall bakery-style treat.

Print Recipe Pin Recipe

Prep Time 15 minutes mins

Cook Time 20 minutes mins

Total Time 35 minutes mins

Servings: 12 muffins

Course: Breakfast, Dessert, Snack

Cuisine: American, Fall

Calories: 280

Ingredients

  

Pumpkin Muffin Batter

• 1.75 cups all-purpose flour
• 1 cup granulated sugar
• 0.5 cup brown sugar
• 1 tsp baking soda
• 0.5 tsp baking powder
• 1.5 tsp pumpkin pie spice
• 1 tsp cinnamon
• 0.5 tsp salt
• 1 cup pumpkin purée
• 2 eggs
• 0.5 cup vegetable oil
• 0.25 cup milk
• 2 tsp vanilla extract

Cream Cheese Swirl

• 8 oz cream cheese softened
• 0.25 cup granulated sugar
• 1 tsp vanilla extract
• 1 egg yolk

Equipment

• Mixing bowls
• Whisk
• 12-cup muffin pan
• Muffin liners

Method

 

1. Preheat oven to 350°F and line muffin pan with liners.
2. Whisk dry ingredients together in a large bowl.
3. Whisk pumpkin, eggs, oil, milk, and vanilla in a separate bowl.
4. Combine wet and dry ingredients until just mixed.
5. Beat cream cheese, sugar, vanilla, and egg yolk until smooth.
6. Divide pumpkin batter into muffin cups.
7. Add 1 tbsp cream cheese mixture to each and swirl gently.
8. Bake 18–22 minutes until set.
9. Cool before serving.

Notes

For bakery-style high tops, start at 375°F for 5 minutes, then reduce to 350°F.

Tips for Perfect Pumpkin Cream Cheese Muffins

Use room-temperature cream cheese

This ensures a smooth, easily swirled topping.

Don’t overmix

Overmixing leads to dense muffins — stop as soon as the batter comes together.

For higher muffin tops

Start baking at 375°F for 5 minutes, then drop to 350°F for the remaining time.

Swirl gently

Overmixing the swirl can muddy the design.

Freeze for later

Store individually wrapped muffins in the freezer up to 2 months.

Variations

Pumpkin Chocolate Chip Cream Cheese Muffins

Add 1 cup mini chocolate chips to the batter.

Maple Cream Cheese Swirl

Replace sugar in cream cheese with 3 tbsp maple syrup.

Cinnamon Crunch Topping

Sprinkle cinnamon-sugar on top before baking for bakery-style sparkle.

Nutty Pumpkin Muffins

Add chopped pecans or walnuts to the batter.

How to Serve

• Warm with butter
• With a latte or hot chocolate
• As a fall brunch item
• Packed for school or work
• As a Thanksgiving breakfast treat

They taste best the next morning when the flavors settle into the perfect pumpkin-cheesecake balance.

Storage

Room Temp: 2 days
Refrigerator: 5 days
Freezer: 2 months

Reheat in microwave for 10–12 seconds.