Pumpkin Cheesecake Muffins (Small Batch)

Fall is the perfect time to indulge in cozy, spiced treats, and these Pumpkin Cheesecake Muffins check all the boxes. They’re tender, moist, and infused with warming pumpkin pie spice, with a luscious swirl of cheesecake both inside the muffin and on top.

Best of all, this is a small-batch recipe that yields just six muffins—ideal for enjoying a seasonal treat without having leftovers sitting around for days.

This recipe strikes the perfect balance between sweet pumpkin muffin and creamy cheesecake, making each bite rich and indulgent while still light and fluffy. If you’re looking for a bakery-worthy fall recipe you can whip up in your own kitchen, this one is a must-try.

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My Opinion

I absolutely loved making these muffins because they felt like such a seasonal treat with minimal fuss. The batter came together so easily, and the cheesecake swirl made them look as if they came straight from a bakery display case.

I found the texture of the muffins to be perfectly moist thanks to the pumpkin puree and Greek yogurt, and the cheesecake filling added just the right amount of creaminess to balance the warm spices.

The small batch size was another bonus. Sometimes I hesitate to make desserts because I don’t want a huge pan of sweets sitting around, but this recipe made just enough to enjoy fresh for a couple of days without waste.

Honestly, these muffins didn’t last long in my kitchen—every time I walked by the counter, I found myself reaching for another. They’ve definitely earned a spot in my favorite fall bakes.

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Why You’ll Love This Recipe

• 🎃 Perfectly seasonal: Full of pumpkin spice flavor, ideal for fall baking.
• 🧁 Small batch: Makes 6 muffins, perfect for 1–2 people or a small household.
• ✨ Bakery-style look: Tall, domed tops with a gorgeous swirl of cheesecake.
• 💛 Moist & tender: Made with oil and pumpkin puree for an extra soft texture.
• 🍰 Double cheesecake layer: Not just cream cheese—this is a true cheesecake swirl inside and on top.

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Tools You’ll Need

• Muffin tin (6-cup or standard 12-cup with alternate cups filled)
• Parchment muffin liners
• Mixing bowls (one for cheesecake filling, one for muffin batter)
• Hand mixer or whisk
• Measuring cups or kitchen scale (grams preferred for accuracy)
• Piping bag (or zip-top bag for the cheesecake swirl)
• Toothpick (for doneness testing)

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Ingredients

Cheesecake Filling

• 120 g (½ cup) cream cheese, room temperature
• 25 g (2 tbsp) granulated sugar
• 1 egg yolk, room temperature
• ½ tsp vanilla extract

Pumpkin Muffins

• 50 g (¼ cup) vegetable oil (or neutral oil of choice)
• 100 g (½ cup) granulated sugar
• 1 large egg, room temperature
• 30 g (2 tbsp) Greek yogurt (or sour cream), room temperature
• 150 g (⅔ cup) canned pumpkin puree (100% pure pumpkin)
• 1 tsp pumpkin pie spice (or cinnamon as substitute)
• 120 g (1 cup) all-purpose flour
• 1 tsp baking powder
• ¼ tsp baking soda
• ¼ tsp salt

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Step-by-Step Instructions

1. Preheat the oven
   Set your oven to 425°F (220°C). Line a muffin tin with 6 parchment liners, alternating cups to allow space for the muffins to rise with tall, domed tops.
2. Prepare the Cheesecake Filling
   In a small bowl, beat together the cream cheese and sugar until smooth and creamy. Add the egg yolk and vanilla, mixing until fully combined. Transfer the mixture into a piping bag (or zip-top bag with the tip cut off). Set aside.
3. Make the Muffin Batter
   In another mixing bowl, whisk together the oil, sugar, egg, Greek yogurt, pumpkin puree, and pumpkin pie spice until smooth and cohesive.
   In a separate bowl, combine the flour, baking powder, baking soda, and salt. Gently fold the dry mixture into the wet ingredients, mixing only until no streaks of flour remain. Be careful not to overmix, as this can lead to tough muffins.
4. Assemble the Muffins
   Divide the pumpkin muffin batter evenly among the six muffin liners, filling nearly to the top. Pipe the cheesecake filling into the center of each muffin, pushing slightly down into the batter. Continue piping until the cheesecake layer reaches the top, then swirl slightly for a marbled effect.
5. Bake the Muffins
   Bake at 425°F (220°C) for 5 minutes, then reduce the oven temperature to 350°F (175°C) without opening the oven door. Continue baking for 10–15 more minutes, or until a toothpick inserted into the muffin (avoiding the cheesecake swirl) comes out with only a few moist crumbs.
6. Cool and Serve
   Allow the muffins to cool in the pan for 5–10 minutes before transferring them to a wire rack. Enjoy warm, or let them cool completely for a firmer cheesecake layer.

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Expert Baking Tips

• Weigh your ingredients: A kitchen scale ensures accuracy and consistency.
• Room temperature ingredients: Helps everything mix together smoothly.
• Don’t overmix: Gentle mixing keeps muffins soft and tender.
• Check early: Start testing at 14 minutes; muffins can go from underdone to overdone quickly.
• Bakery-style muffin tops: The high initial temperature (425°F) helps the muffins rise tall before lowering the heat to bake through.

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Variations & Q&A

Can I double this recipe?
Yes! Double all ingredients for 12 muffins. For best results, use a kitchen scale to measure.

Can I substitute the Greek yogurt?
Yes—regular yogurt or sour cream both work well.

What if I don’t have pumpkin pie spice?
Use the same amount of cinnamon, or make your own mix with cinnamon, nutmeg, ginger, and cloves.

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Storage Notes

• Best enjoyed the day they’re baked for maximum freshness.
• Store leftovers in an airtight container at room temperature for up to 3 days.
• For longer storage, refrigerate for up to 5 days or freeze for up to 2 months. Thaw overnight before serving.

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Conclusion

These Pumpkin Cheesecake Muffins bring together the cozy warmth of pumpkin spice with the indulgence of cheesecake in every bite. With their small-batch yield, they’re perfect for enjoying a seasonal treat without overbaking.

Easy, moist, and visually stunning, these muffins are guaranteed to become a fall favorite in your kitchen.

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Category: Dessert, Fall Baking, Muffins

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