Pumpkin cheesecake muffins are a delightful fall-inspired treat that combines the rich, spiced flavors of pumpkin swirled with the creamy goodness of cheesecake.

An overhead view of Libby's cheesecake pumpkin muffins and two mini pumpkins sitting next to them.

Pumpkin cheesecake muffins are perfect for breakfast, brunch, or a sweet snack with a cup of hot coffee on a crisp autumn morning.

The base of these muffins is a moist, spiced pumpkin batter that captures the essence of fall. Each bite is a harmonious blend of pumpkin puree, warm spices like cinnamon and pumpkin pie spice, and a hint of nutmeg.

The texture is incredibly tender, ensuring that every bite is a soft, comforting experience.

But what truly elevates these classic pumpkin muffins to a new level of indulgence is a rich and velvety cream cheese swirl.

Enjoy the wonderful combination of delicious pumpkin cream cheese muffins in every bite this fall season!

Want more fall desserts? Check out these fun fall cupcakes and 32 Easy Pumpkin Desserts Made with Canned Pumpkin Purée!

A dark table with Libby's cheesecake pumpkin muffins and two mini pumpkins sitting in the middle of all the muffins. One muffin at the bottom of the photo is sliced in half showing the cheesecake filling.

Ingredients for Pumpkin Cheesecake Muffins

Can of Libby’s Pumpkin Puree or Homemade Pumpkin Puree
Canola or Vegetable Oil
Milk
White Granulated Sugar
Light Brown Sugar
Large Eggs
Egg Yolk
All-Purpose Flour
Pumpkin Pie Spice
Ground Cinnamon
Ground Nutmeg
Baking Soda
Salt
Cream Cheese
Pure Vanilla Extract

How to Make Pumpkin Cheesecake Muffins

Preheat oven to 350 degrees Fahrenheit. Line the muffin pan with 24 muffin liners.

Two egg yolks, pumpkin puree, and sugar in a silver mixing bowl of an electric mixer with a white paddle attachment.

Pumpkin muffin batter in an electric mixer with a white paddle attachment.

In a large mixing bowl or an electric mixer with a paddle attachment, mix together pumpkin puree, canola oil, milk, white granulated sugar, brown sugar, and eggs.
In a separate large bowl, sift or whisk together dry ingredients – combine flour, pumpkin pie spice, ground cinnamon, nutmeg, baking soda, and salt. Slowly add the flour mixture to the wet ingredients until well blended.
In a medium bowl, add cheesecake batter ingredients and use an electric hand mixer to blend.

A white large bowl with a hand mixer and cheesecake filling sitting inside of it. A muffin pan sits in the background with pumpkin batter in each tin.

Two muffin tins sitting side by side. The one on the right is entirely in view while the other only shows a small portion of the pan. The tins of the pan are filled with pumpkin muffin batter.

In another bowl, use a handheld mixer to combine cheesecake batter ingredients. Add it to an icing bag and push the tip into the pumpkin batter. Pull up while squeezing the bag to fill the centers.
Bake in the oven for 18-20 minutes. Check for doneness by inserting a toothpick in the center of a muffin and seeing if it comes out clean. If it does, remove it from the oven and place it on a wire rack.

An overhead view of a muffin pan with 12 tins filled with 12 white cupcake liners, pumpkin muffin batter, and cheesecake filling in the center of each.

An overhead view of a muffin pan with 12 tins filled with 12 white cupcake liners and 12 Libby's pumpkin cheesecake muffins.

Can also check for doneness by lightly pressing the top of the muffins. If it sinks, bake a little longer. If it bounces back, they’re done.

Variations of Pumpkin Cheesecake Muffins

Pumpkin cheesecake muffins are a delicious treat on their own, but there are various ways to add unique twists and variations to the classic recipe. Here are some creative variations of pumpkin cheesecake muffins:

Streusel Topping: Add a crumbly streusel topping to your muffins for extra texture and flavor. A typical streusel includes butter, brown sugar, flour, and spices like cinnamon and nutmeg.

Chocolate Chip: Fold chocolate chips into the pumpkin muffin batter for a delightful combination of pumpkin and chocolate flavors. You can also use white chocolate chips or butterscotch chips for a different twist.

A side view of a muffin pan with Libby's cheesecake pumpkin muffins next to mini pumpkins.

Nutty Delight: Mix chopped nuts like pecans or walnuts into the muffin batter for a crunchy texture and nutty flavor. You can also sprinkle some on top for extra crunch.

Swirls of Caramel: Drizzle caramel sauce into the muffin batter or create a caramel swirl within the muffins for a sweet, gooey surprise.

Gingerbread Spice: Enhance the spice profile with ginger, cloves, and allspice for a gingerbread-inspired twist. These spices complement the pumpkin and cheesecake flavors beautifully.

Pumpkin Spice Latte: Add instant coffee or espresso powder to the muffin batter to create a “pumpkin spice latte” flavor. You can even add a coffee-flavored cheesecake filling.

Maple Glaze: Top your muffins with a luscious maple glaze for a rich, autumn-inspired twist that makes them extra moist pumpkin muffins. The glaze can be made with maple syrup, powdered sugar, and a touch of milk.

An overhead view of Libby's cheesecake pumpkin muffins and three mini pumpkins sitting next to them.

How to Store Pumpkin Cheesecake Muffins

Room Temperature: Pumpkin cheesecake muffins can be stored at room temperature for about 3 days.

However, they should be kept in an airtight container to maintain freshness. After this time, they may start to become less moist and lose their quality.

Refrigeration: If you want to extend the shelf life, you can store pumpkin cheesecake muffins in the refrigerator. When stored in an airtight container in the fridge, they can last for about 5-7 days. The cold temperature helps slow down the growth of bacteria and molds.

Freezing: To keep pumpkin cheesecake muffins for an extended period, you can freeze them. Place them in an airtight container or freezer bag. They can last in the freezer for up to 2-3 months.

They are safe to eat beyond this time if stored properly, but their texture and flavor may gradually decline over an extended period.

When you’re ready to enjoy them, simply thaw them in the refrigerator or at room temperature.

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