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Irresistible Pumpkin Cheesecake Swirl Muffins – Perfectly Spiced & Creamy | The Ultimate Fall Treat

Fall baking wouldn’t be complete without the cozy warmth of pumpkin spice, and these Pumpkin Cheesecake Swirl Muffins are the ultimate seasonal treat. They combine the best of both worlds: soft, spiced pumpkin muffins and a luscious cheesecake swirl that melts into every bite. The result? A muffin that’s creamy, tender, and full of warm autumn flavor. These muffins are perfect for breakfast, brunch, afternoon snacks, or even as a not-too-sweet dessert. The pumpkin muffin base is moist and lightly spiced, and the cheesecake layer adds a tangy, creamy contrast that makes them irresistible. Not only are they simple to make, but they also store well and are perfect for sharing. Whether you’re cozying up with a hot drink or bringing something special to a fall gathering, these muffins are sure to impress.
Prep Time 15 minutes
bake time 20 minutes
Total Time 35 minutes
Servings: 12 muffins

Ingredients
  

Fruits & Vegetables:
  • 1 cup pumpkin puree not pumpkin pie filling
Fresh Ingredients:
  • 2 eggs
  • 1 egg yolk
Culinary Aids & Spices:
  • cups all-purpose flour
  • 1 teaspoon baking soda
  • ¼ cup brown sugar packed
  • 1 cup granulated sugar divided for muffin and cheesecake
  • ½ teaspoon cinnamon
  • 2 teaspoons pumpkin pie spice
  • ¼ teaspoon salt
  • teaspoons vanilla extract divided
Oils & Vinegars:
  • ½ cup vegetable oil
Dairy Products:
  • 6 oz cream cheese softened

Equipment

  • You won’t need any special equipment to bake these muffins, just a few kitchen basics:
  • Muffin tin (12-cup)
  • Paper muffin liners (optional but recommended)
  • Mixing bowls (large and medium)
  • Whisk
  • Hand or stand mixer
  • Rubber spatula
  • Spoon or cookie scoop
  • Measuring cups and spoons
  • Toothpick (for testing doneness and swirling)

Method
 

Step 1: Preheat and Prep
  1. Preheat your oven to 350°F (175°C).
  2. Line a standard 12-cup muffin tin with paper liners or lightly grease with oil or spray.
Step 2: Make the Muffin Batter
  1. In a large mixing bowl, whisk together:
  2. 1 cup pumpkin puree
  3. 2 eggs
  4. ½ cup vegetable oil
  5. ¾ cup of the granulated sugar
  6. ¼ cup brown sugar
  7. 1 teaspoon of vanilla extract
  8. Stir until smooth and fully combined.
  9. In another bowl, whisk together:
  10. 1½ cups all-purpose flour
  11. 1 teaspoon baking soda
  12. ½ teaspoon cinnamon
  13. 2 teaspoons pumpkin pie spice
  14. ¼ teaspoon salt
  15. Gradually add the dry ingredients to the wet ingredients and stir until just combined. Do not overmix.
Step 3: Make the Cheesecake Swirl
  1. In a medium bowl, beat together:
  2. 6 oz cream cheese, softened
  3. 1 egg yolk
  4. ¼ cup granulated sugar
  5. ½ teaspoon vanilla extract
  6. Mix until smooth and creamy.
Step 4: Fill the Muffin Cups
  1. Spoon the pumpkin muffin batter evenly into each muffin cup, filling them about ¾ full.
  2. Add a teaspoon of cheesecake mixture on top of each.
  3. Use a toothpick or small knife to gently swirl the cheesecake into the batter.
Step 5: Bake
  1. Bake in the preheated oven for 18–22 minutes, or until a toothpick inserted in the center comes out clean (except where there’s cheesecake).
  2. The tops should be set and slightly golden.
Step 6: Cool
  1. Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.

Notes

🧊 Storage & Reheating
Room Temperature: Store in an airtight container for up to 2 days.
Refrigerator: Keep in a sealed container for up to 5 days to preserve the cheesecake layer.
Freezer: Freeze muffins individually wrapped for up to 2 months. Thaw overnight in the fridge or warm in the microwave for 20–30 seconds.
To Reheat:
Microwave for 15–20 seconds.
Or warm in the oven at 300°F (150°C) for 5–7 minutes.
🥄 Variations
Switch things up with these delicious twists on the classic pumpkin cheesecake swirl muffin:
Mini Muffins: Make bite-sized treats by baking in a mini muffin tin. Adjust bake time to 10–12 minutes.
Chocolate Chip Pumpkin Muffins: Fold ½ cup of mini chocolate chips into the pumpkin batter.
Nutty Crunch: Add a sprinkle of chopped pecans or walnuts to the top before baking.
Spiced Topping: Mix brown sugar and cinnamon and sprinkle over the cheesecake swirl for a crunchy top.
Coconut Twist: Add shredded coconut to the pumpkin batter for tropical flair.
Maple Infused: Add 1 tablespoon pure maple syrup to the cream cheese mixture.
Gluten-Free: Substitute a 1:1 gluten-free flour blend for the all-purpose flour.
Dairy-Free: Use vegan cream cheese and plant-based oil for a dairy-free option.
Sugar-Free: Replace sugar with a natural sweetener blend like monk fruit or erythritol (adjust to taste).
❓ 10 FAQs
1. Can I use canned pumpkin pie filling?
No—use pure pumpkin puree. Pumpkin pie filling contains added spices and sugar which would throw off the balance.
2. What’s the best way to swirl the cheesecake?
Use a toothpick, skewer, or butter knife and gently swirl in a figure-eight motion without overmixing.
3. Can I double this recipe?
Absolutely! Just prepare two muffin trays and rotate them halfway through baking for even results.
4. Can I use store-bought pumpkin pie spice?
Yes! That’s exactly what this recipe uses—it's a blend of warm spices perfect for fall baking.
5. How can I tell when they’re done?
Insert a toothpick in the center; it should come out clean of muffin batter. The cheesecake part may look moist, which is normal.
6. Can I make this in a loaf pan?
Yes! Pour into a greased loaf pan and bake at 350°F for 45–55 minutes. Cover the top if it browns too quickly.
7. How do I keep the cream cheese from sinking?
Make sure the muffin batter is thick enough, and avoid overmixing the swirl. Placing the cheesecake swirl gently on top also helps.
8. Can I use melted butter instead of oil?
Yes, but the texture may be a little more dense. Vegetable oil keeps the muffins soft and moist.
9. What if I don’t have pumpkin pie spice?
Make your own: Mix 1 tsp cinnamon, ¼ tsp nutmeg, ¼ tsp ginger, and ⅛ tsp cloves.
10. Are these muffins freezer-friendly?
Absolutely! Wrap each muffin in plastic wrap, then freeze in a zip-top bag. Thaw or reheat as needed.
🏁 Conclusion
These Pumpkin Cheesecake Swirl Muffins are a dreamy mash-up of soft, spiced pumpkin muffins and rich, creamy cheesecake topping. They bake up tender and flavorful, perfect for cozy mornings, autumn get-togethers, or sweet afternoon breaks.
The combination of warm spices, pumpkin richness, and tangy cream cheese is hard to resist. Plus, they’re easy to make and freeze beautifully. This recipe deserves a spot in your fall baking rotation—you won’t regret it!