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Most cream cheese muffins have a filling that melts right into the batter. Mine bakes up like a mini cheesecake in the center of every muffin. The secret is an egg yolk and a quick chill in the freezer. Pair that with my spiced pumpkin muffin base and you get the best of both.
My family was WOWed by these! These have the warm cozy spices and then the perfect tanginess from the cream cheese…YUM. I added the crumble top from your other pumpkin muffin recipe and oh my goodness. Hello new staple in my house!!
-Kayla
Why You’ll Love These Pumpkin Cream Cheese Muffins
I spent 6 months testing muffin recipes for my Bakery Style Muffins Cookbook, and that’s where I learned how to get tall, domed tops every time. This recipe is a mash up of two of my favorites: my pumpkin muffins and my triple berry cheesecake muffins. The pumpkin base stays exactly the same. The filling comes straight from the cheesecake muffins, and that filling is what makes these special.
Most cream cheese fillings are just sweetened cream cheese, and they melt into the batter as they bake. Cream cheese and sugar loosen when heated, so the filling sinks, spreads, or blurs into the crumb. Mine has one extra ingredient: an egg yolk. The yolk proteins set during baking, so the filling holds its shape as a distinct pocket of cheesecake.
The yolk also keeps the filling smooth and creamy, with a custardy, cheesecake-like bite instead of something grainy or greasy. It adds richness too, plus a slightly golden color so the filling looks finished. I use only the yolk because the white is mostly water and sets firm and rubbery. In a small batch of filling, a whole egg makes it puff, weep, or turn spongy.
The last step is chilling. The filling goes in the freezer while you make the batter, and that cold start helps keep it from melting into the muffins. Put it all together and every muffin has a tall, spiced pumpkin top with a creamy pocket of cheesecake right in the center.
Ingredients You’ll Need for Cream Cheese Pumpkin Muffins
Cream cheese-stuffed pumpkin muffins? Yes, please! These muffins are made with surprisingly simple ingredients. Get the full recipe with measurements and ingredients in the recipe card below. Here’s what you’ll need:
- All-purpose flour: Make it gluten-free by using a 1:1 gluten-free baking flour.
- Granulated sugar
- Baking powder
- Baking soda
- Salt
- Ground cinnamon
- Ground nutmeg
- Ground ginger
- Pure pumpkin puree: 100% pure pumpkin canned
- Eggs
- Vegetable oil
- Milk
Cream Cheese Layer
- Cream cheese: room temperature
- Egg yolk
- Granulated sugar
- Vanilla extract
How to Make Pumpkin Cream Cheese Muffins
These delicious pumpkin cream cheese muffins look like they came from a bakery, but you will be able to make them from home with success when you follow my easy step-by-step instructions below. Keep reading for the full recipe in the recipe card below. Here are the easy steps:
How to Make Cream Cheese Layer
- Mix and chill cream cheese layer. Place the cream cheese, egg yolk, sugar, and vanilla extract in a mixing bowl and beat with an electric mixer for 1-2 minutes, until smooth. Place the bowl in the freezer while you prep the rest of the recipe. Chilling the filling will help keep it from melting into the muffins.
How to Make Muffins
- Mix dry ingredients. In a large bowl combine the flour, granulated sugar, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger. Stir together and set aside.
- Mix wet ingredients. In a larger mixing bowl combine the pumpkin, eggs, vegetable oil, and milk. Stir to combine.
- Combine wet and dry ingredients. Gradually mix the dry ingredients into the wet ingredients, mixing just until combined. The batter will be very thick.
- Rest batter and prep oven. Cover the bowl with a towel and allow the batter to rest for 15 minutes. During this time, preheat the oven to 425ºF / 220ºC.
- Prep muffin pan. For bakery style muffins, line a 12 count muffin pan with 6 muffin liners, meaning you’ll only fill every other muffin well with batter. For the photos, I used tulip muffin liners, you can find them on amazon. Tulip liners naturally produce a taller muffin so you don’t need to do the every other muffin method. If you’re using regular muffin liners, I recommend filling every other muffin well.
- Assemble muffins. Fill the muffin cups with 2 tablespoons of batter. Drop 1 tbsp of the cream cheese mixture into each muffin cup. Use a toothpick to swirl into the batter. Then add 6 tablespoons of batter, covering the cream cheese. Top each muffin with ½ tbsp of cream cheese, swirling with a toothpick. Sprinkle the tops of the muffins with sanding sugar.
- Bake and cool. While one pan is baking, refrigerate the remaining batter in the bowl. Place one pan in the center of the oven and bake for 7 minutes at 425ºF / 220ºC, then keep the muffins in the oven, turn the temperature down to 350ºF / 180ºC and bake for 18-21 minutes if using regular muffin liners / bake for 20-25 minutes if using tulip muffin liners or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan. Repeat with the remaining batter, bumping the temperature back up to 425ºF / 220ºC.
Tips for the Best Pumpkin Cheesecake Muffins
- Use room temperature cream cheese. Cold cream cheese won’t beat smooth, and you’ll end up with lumps in the filling.
- Chill the filling. Pop it in the freezer while you make the batter. Cold filling holds its shape in the oven instead of melting into the muffin.
- Layer it in. Start with batter, add the filling, swirl, then cover it with more batter. That bottom layer keeps the filling centered instead of sitting at the base of the liner.
- Pick your liner. I used tulip liners in the photos, so I filled every cup in the pan. Tulip liners bake differently than regular liners. If you’re using regular liners, fill every other cup and fill them to the top for tall, bakery style domes. Either works, so go with what you like.
Pumpkin Cream Cheese Muffin Variations
If you love indulging in pumpkin recipes during Fall season, or any time of year, you are going to be hooked on these muffins! Here are some swaps if you need or want to change the recipe:
- Gluten-free Pumpkin Cream Cheese Muffins: I’ve made these muffins with both regular all-purpose flour and gluten free flour with awesome results on multiple occasions. I recommend King Arthur’s Gluten Free Measure for Measure Flour. Use it as a one for one substitute for regular flour.
- Skip the cream cheese layer: If you just want pumpkin muffins without the cream cheese, use my pumpkin muffins recipe.
- Vegan Pumpkin Cream Cheese Muffins: Substitute dairy cream cheese with a plant-based cream cheese alternative and use flax eggs (ground flaxseed + water) in place of eggs. I have not tested this so I can’t attest to how this turns out.
- Pumpkin Cream Cheese Streusel Muffins: Top the muffins with a buttery crumb topping.
- Add nuts: Add chopped nuts (like pecans or walnuts) to the batter or as a topping for added crunch and texture.
- Chocolate Chip Pumpkin Cream Cheese Muffins: Fold in some chocolate chips to the muffin batter or the cream cheese filling for a sweeter, more indulgent muffin.
How to Serve Pumpkin Cream Cheese Muffins
Another great thing about these muffins is that they are great warm, cold and room temperature. You just can’t go wrong!
You can serve these with a cup of coffee, tea, hot chocolate or to really go all out on the Fall theme, a cup of warm apple cider.
How to Store and Freeze Pumpkin Cream Cheese Muffins
Because these muffins have a cream cheese filling, they need to go in the fridge. If you’ll eat them within a few hours of baking, they’re fine on the counter. Anything longer, refrigerate them.
The fridge can make muffins soggy, and those tops can lose their crunch in an airtight container. But I have a trick to help with that: paper towels.
Line the bottom of an airtight container with paper towels. Place the muffins in a single layer, then cover them with another layer of paper towels. The paper towels act like a sponge and soak up the moisture the muffins release.
Store them in the fridge for up to 3 days. If the paper towels get too damp, swap in fresh ones. Let the muffins sit out for a few minutes before eating, or warm them in the microwave for a few seconds.
How to Freeze Muffins
Individually wrap each muffin in plastic wrap. Then place them in a zip top bag or airtight container and freeze for up to 3 months.
To thaw, leave them at room temperature until defrosted, about 1 hour. Or unwrap them and microwave in 20 second intervals until warm.
I added the last line of the storage section (let them sit out or warm them up before eating). Cut it if that’s not how you serve them.
Pumpkin Cream Cheese Muffins FAQs
Yes. Because of the cream cheese filling, store them in the fridge if you won’t eat them within a few hours.
Usually the filling was too warm or too loose. Chill it in the freezer while you prep the batter, and don’t skip the egg yolk, because it helps the filling set as it bakes. Start with a layer of batter under the filling so it has something to sit on.
Yes. Bake at 425ºF for the first 5 minutes, then lower to 400ºF for the remaining 5 to 10 minutes, possibly longer depending on how full you fill them. If you overfill the cups, use the every other cup method. If not, fill the whole pan.
Yes. Fill the pans ¾ full and bake at 350ºF the whole time. Start checking at 30 minutes, but expect closer to 35 to 40 minutes depending on pan size.
More Pumpkin Recipes
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Pumpkin Cheesecake Muffins
Video
Ingredients
- 3 cups (360g) all-purpose flour
- 1 ¾ cups (350g) granulated sugar
- 3 tsp baking powder
- ½ tsp baking soda
- 1 tsp salt
- 3 tsp ground cinnamon
- ¼ tsp ground nutmeg
- ¼ tsp ground ginger
- 1 15 oz can (425g) 100% pure pumpkin puree
- 2 large eggs
- ¾ cup (170g) vegetable oil
- ½ cup (113g) milk
Cream Cheese Layer
- 8 oz (227g) cream cheese, room temperature
- 1 egg yolk
- ½ cup (100g) granulated sugar
- 2 tsp vanilla extract
Instructions
Cream Cheese Layer
- Place the cream cheese, egg yolk, sugar, and vanilla extract in a mixing bowl and beat with an electric mixer for 1-2 minutes, until smooth. Place the bowl in the freezer while you prep the rest of the recipe. Chilling the filling will help keep it from melting into the muffins.8 oz (227g) cream cheese, 1 egg yolk, ½ cup (100g) granulated sugar, 2 tsp vanilla extract
Muffins
- In a mixing bowl combine the flour, granulated sugar, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger. Stir together and set aside.3 cups (360g) all-purpose flour, 1 ¾ cups (350g) granulated sugar, 3 tsp baking powder, ½ tsp baking soda, 1 tsp salt, 3 tsp ground cinnamon, ¼ tsp ground nutmeg, ¼ tsp ground ginger
- In a larger mixing bowl combine the pumpkin, eggs, vegetable oil, and milk. Stir to combine.1 15 oz can (425g) 100% pure pumpkin puree, 2 large eggs, ¾ cup (170g) vegetable oil, ½ cup (113g) milk
- Gradually mix the dry ingredients into the wet ingredients, mixing just until combined. The batter will be very thick.
- Cover the bowl with a towel and allow the batter to rest for 15 minutes. During this time, preheat the oven to 425ºF / 220ºC.
- For bakery style muffins, line a 12 count muffin pan with 6 muffin liners, meaning you’ll only fill every other muffin well with batter. For the photos, I used tulip muffin liners, you can find them on amazon. Tulip liners naturally produce a taller muffin so you don’t need to do the every other muffin method. If you’re using regular muffin liners, I recommend filling every other muffin well.
- Fill the liners with 2 tablespoons of batter. Drop 1 tbsp of the cream cheese mixture into each muffin cup. Use a toothpick to swirl into the batter. Then add 6 tablespoons of batter, covering the cream cheese. Top each muffin with ½ tbsp of cream cheese, swirling with a toothpick. Sprinkle the tops with sanding sugar.
- While one pan is baking, refrigerate the remaining batter in the bowl. Place one pan in the center of the oven and bake for 7 minutes at 425ºF / 220ºC, then keep the muffins in the oven, turn the temperature down to 350ºF / 180ºC and bake for 18-21 minutes if using regular muffin liners / bake for 20-25 minutes if using tulip muffin liners or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan. Repeat with the remaining batter, bumping the temperature back up to 425ºF / 220ºC.
Last Step: I’d love to hear what you think. Leave a rating and comment here.
My family was WOWed by these! These have the warm cozy spices and then the perfect tanginess from the cream cheese…YUM. I added the crumble top from your other pumpkin muffin recipe and oh my goodness. Hello new staple in my house!!
Do you use the extra egg white? Your recipes with cream cheese say to use egg yolk with the filling…do you use the egg white in the other portion of the batter or leave it out?
You don’t use the egg white.
Wow!!!! I’m about to make these for third time this week! My family loves this recipe 😍
Wow!!!! I’m about to make these for third time this week! My family loves this recipe 😍
The taste is great. I wish I would have seen the video first. Scooping tablespoons of batter and filling…pass. I made them GF using KA flour so had to let the batter rest for 30 minutes which firmed the cream cheese filling. Next time I’m going to use the larger cupcake liners and not refrigerate the cream cheese filling which will help mixing with the toothpick. Definitely worth a try.
The best ever!
I do not have vegetable oil on hand, can I sub for coconut oil?
You can use any neutral oil!
The BEST muffins I have made so far! Amazing recipe! My first muffins like bakery of my dream. Thanks a lot for sharing your work! 🙏
Can you use whole wheat flour? I want to add a little more fiber.
Hi Ally! I personally haven’t tried baking with whole wheat flour so I can’t offer an accurate answer about how it would turn out.
I only have regular muffin liners aswell as regular muffin tins do I still have too line every other one ? Or can i do everyone ?
Yes! My recipes actually only work for regular muffin tins! As far as the liners go, that’s total preference whether to use regular liners or tulip liners. Still do every other one so that the muffins have room to spread and dome!