Small Batch Pumpkin Cheesecake Muffins

Yield: 6 pumpkin cheesecake muffins // Total Time: 40 min. // Disclaimer: This post includes affiliate links.

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

Small batch pumpkin cheesecake muffins

If you’re looking for delicious fall bakes that won’t leave you with tons of leftovers, you’ve come to the right place. These small batch pumpkin cheesecake muffins make just 6 muffins, are seriously delicious, and easier to make than you might think! We start with a tender and moist pumpkin muffin, then we put a layer of cheesecake inside the muffins and swirl some on top. It’s an easy and delicious way to level up your standard pumpkin muffin!

Small batch pumpkin cheesecake muffins recipe tips

Weigh your ingredients

Weighing your ingredients is important for getting the recipe perfect and getting consistent results. Not weighing your ingredients can lead to adding too much or too little of an ingredient. In a small batch recipe it is especially important to get those correct measurements because there is less room for error. If you haven’t already, I highly recommend purchasing a kitchen scale. This one is super cheap and worked well for me when I was starting out!

Mix the batter carefully

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

Room temperature ingredients

It is important for the ingredients to be at room temperature so that they properly incorporate with each other. If you have ever had your batter look curdled, it is most likely due to the ingredients separating from being at different temperatures. Take out the eggs, sour cream, and cream cheese least 30 minutes and up to 1 hr 30 min. before starting the recipe OR follow these methods for room temperature ingredients FAST:

1. Fast room temperature eggs. Place the eggs in a bowl in the sink and continuously run hot water over it for one minute. And there you go – room temperature eggs! Alternatively (and less waste-fully) fill a bowl with warm water and let the eggs sit in it for 5 minutes.
2. Fast room temperature sour cream. Microwave the sour cream in 5 second intervals until it is no longer cold (but not hot!). And there you go – fast and easy room temperature sour cream!
3. Fast room temperature cream cheese. Slice the cream cheese into thin slices and place them flat on a plate. Microwave in 5 second intervals until the cream cheese is soft, but not too warm. Proceed with your room temp. cream cheese!

Keep an eye on those pumpkin cheesecake muffins!

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.

Get those perfect muffin tops

The 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!

Get evenly distributed 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.

Ingredients and substitutions

For the 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: for tenderizing the muffins. You can use any neutral oil, such as canola, here as well.

Granulated sugar: for sweetening and helping lock in moisture.

Brown sugar: for sweetening, flavor, and adding moisture to the muffins. For fall bakes I like to use dark brown sugar just for that extra molasses flavor, but light brown sugar works here as well.

Canned pumpkin: for flavor! Make sure you are using 100% pure pumpkin.

Egg: for binding and for moisture.

Sour cream: for moisture and tenderizing the muffin batter. You can also substitute in greek yogurt here!

For the 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: for flavor. I use and love this vanilla extract!

How to make small batch pumpkin cheesecake muffins

1. Make the cheesecake filling. In a small bowl, beat the cream cheese with a fork until smooth. Then, whisk in the egg yolk, sugar, and vanilla until combined. Set aside.

2. Mix the oil and sugars. In a small mixing bowl, whisk together the oil, brown sugar, and granulated sugar. The mixture will look a little dry and crumbly, that is normal!

3. Add wet ingredients. Add in the pumpkin, egg, and sour cream. Whisk until thoroughly combined.

4. Mix in dry ingredients. Add in the flour, baking powder, baking soda, salt, and pumpkin pie spice. Gently mix the ingredients together just until no flour streaks remain.

5. Transfer the batter to the muffin pan. Place ~2 tbsp. of batter in each muffin tin, using a spoon to smooth it out as needed. Top each muffin with 1 tbsp. of cheesecake filling, then smooth it out and distribute the rest of the muffin batter over each muffin evenly. Evenly distribute the remaining cheesecake filling over each muffin, then use a toothpick to swirl it around.

5. Bake. We’ll start the muffins out at 425°F for 5 minutes, which will help them rise up nice and tall. Without opening the oven door, reduce the temperature to 350°F / 175°C for the remainder of the baking time.

6. Serve and enjoy! Serve warm or room temperature, both are delicious!

Small batch pumpkin cheesecake muffins Q & A

Can I double these small batch pumpkin cheesecake muffins?

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 pumpkin cheesecake muffins. However, I even more strongly recommend measuring by weight if you are going to double the recipe for the best results.

How to store these muffins

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

A note on oven temperature

Ovens vary and fluctuate in temperature. For example, I always have to set my oven to 330°F if I want it to bake at 350°F. 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.

Tools and ingredients

Muffin pan: I absolutely love USA pan products because of their great quality. This is their muffin pan.

Cookie scoops: A life saver for getting evenly distributed muffins. I have gone through a lot of cookie scoops in my baking journey, and these ones have lasted me the longest without breaking. Plus they are dishwasher safe!

For a full list of tools, equipment and ingredients that I use and love, you can check out this page here.