Light and tender small batch pumpkin muffins swirled with a layer of cheesecake both in the batter and on top of the muffins.

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The pumpkin cheesecake muffins on a plate.

pumpkin cheesecake muffins (small batch)

It’s officially fall which means it’s time for pumpkin everything, which I’m definitely not complaining about. These pumpkin cheesecake muffins are perfectly delicious and super easy to make – they start out with a super moist pumpkin pie spiced pumpkin muffin that’s made with oil so it’s *extra* tender, and they’re filled with a super rich and creamy vanilla cheesecake batter.

why you’ll love these pumpkin cream cheese muffins:

They’re small batch: meaning it makes the perfect amount to have fresh muffins for a few days to yourself.
They’re super moist: as all muffins should be.
The *thick* layer of cheesecake: it’s not just cream cheese in these muffins, it’s a thick layer of cheesecake filling!

expert baking tips

Weigh your ingredients:

My recipes are all written in grams because it is the most accurate way to bake. When you use a kitchen scale, you ensure that your baked goods turn out as close to the written recipe as possible. Plus, the cleanup is way easier when using a scale! I will provide standard cup measurements but please note that I have not tested the recipe using cup measurements and therefore can not guarantee your recipe will come out how mine did. Here is my favorite kitchen scale.

Use room temperature ingredients:

It’s important that your ingredients are at room temperature so that they can easily incorporate with each other. Take out your cold ingredients about an hour before starting the muffins.

Mix the batter carefully

It is super important to not overmix the muffin batter. Overmixing the batter leads to more gluten development which is not desirable in these muffins. Not only will you get those pointy tops on the muffins, but you will end up with tough and chewy muffins.

keep a close eye on the muffins while they bake

Muffins like to go from under-baked to over-baked super quickly so it is important to keep a close eye on them. Start checking at 14 minutes with a toothpick. If the toothpick comes out wet, check them again in 2 minutes and so on until only a few moist crumbs stick to the toothpick.

how to get bakery style muffin tops

One trick to getting those nicely domed muffin tops is (mostly) all in your oven’s temperature! Bake the muffins at 425°F / 220°C for 5 minutes. Then, without opening the oven, reduce the temperature to 350°F / 175°C and continue baking until done. The super high heat will make the muffins rise nice and tall! You will also want to bake them lined in every other tin on the muffin pan, and fill them to the very top. This recipe makes the perfect amount of batter to fill every muffin liner straight to the top for those perfect muffin tops!

Another trick, that’s optional, is resting the muffin batter. After making the muffin batter, let it sit at room temperature for 30 minutes to 1 hour before baking. This will give time for the starches in the flour to absorb the moisture in the batter and will give you more flavorful, higher-rising muffins. Most baking powder is – but – just make sure your baking powder is “double acting” if you try this method.

how to evenly distribute your muffin batter

My favorite way to evenly distribute muffin batter is to use cookie scoops! Works perfectly every time. So long are the days of eyeballing which muffin may need a little more batter.

A note on oven temperature:

Ovens vary and fluctuate in temperature and might not always actually be at the temperature they claim to be at. If you love to bake like I do, I highly recommend getting an oven thermometer. They are super helpful for letting you know when your oven might be lying to you! I use this one.

Close up of one of the pumpkin cheesecake muffins

ingredients for small batch pumpkin cheesecake muffins:

pumpkin muffins:

All purpose flour: for structure and chewiness.
Baking powder: for helping the muffins rise.
Baking soda: for helping the muffins rise.
Salt: to help balance and bring out the sweetness of the muffins.
Pumpkin pie spice: for flavor! I use store-bought pumpkin pie spice but you can also use your own mix if desired. If you don’t want to go out and get pumpkin pie spice, an equal amount of cinnamon will give you some good flavor as well.
Vegetable oil: or any other neutral oil, for tenderizing the muffins.
Granulated sugar: for sweetening and helping lock in moisture.
Canned pumpkin: for flavor! Make sure you are using 100% pure pumpkin.
Egg: for binding and for moisture.
Vanilla extract: for flavor.
Greek yogurt: for moisture and tenderizing the muffin batter. You can also substitute in regular yogurt or sour cream.
Pepitas: optional, for topping and for a little crunch.

cheesecake filling:

Cream cheese: the base of the cheesecake. I recommend using full fat cream cheese, but Neufchatel will work here as well!
Egg yolk: takes the filling from cream cheese to cheesecake consistency.
Granulated sugar: we will only use a little bit of sugar here to sweeten up the cheesecake filling.
Vanilla extract: for flavor.

how to make small batch pumpkin cheesecake muffins

Here’s a few images of the process of making these small batch pumpkin cheesecake muffins. You can find the full recipe at the end of this blog post!

Cheesecake batter in a small mixing bowl.

Beat together the cheesecake ingredients, then set them aside.
In a small mixing bowl, whisk together all of the wet ingredients.

The pumpkin cheesecake muffins in a muffin tin before being baked.

Then mix in the dry ingredients.
Layer the pumpkin muffin batter and the cheesecake batter between six parchment liners. Bake, serve, and enjoy!

small batch pumpkin cheesecake muffins recipe q&a

can I double this recipe?

Of course! Obviously they will not be small batch anymore but small batch isn’t always what we need. Simply double all of the ingredients in the recipe to make 12 delicious muffins. I even more strongly recommend measuring by weight if you are going to double the recipe for the best results.

how to store muffins

Like most baked goods, these muffins will definitely taste the best on the day that they are baked. They will keep well in an airtight container at room temperature for about 3 days.