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Pumpkin cheesecake muffins

It’s pumpkin season and these pumpkin cheesecake muffins are the perfect weekend treat. Full of warm spices, a creamy cheesecake center, and topped with cinnamon sugar, these muffins are so flavorful. They stay moist for days, which makes them a great make ahead option.

I’ll give you variations and substitutions where I can, plus helpful tips and tricks for success. Read on for this info as well as the recipe. If you’d like to skip straight to the recipe, use the jump to recipe button at the top of the post.

You may also be interested in my easy pumpkin muffins and my pumpkin muffin recipe with applesauce. For ease of browsing, you can find all of my muffin recipes in one place.

Pumpkin cheesecake muffins

They are great for a quick breakfast with a cup of coffee or an afternoon/after school snack.

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Why you should make these muffins

They are easy to make – even for beginner bakers, but they are a little more special than a plain muffin. Pumpkin cheesecake muffins have quickly become a new favorite. They are absolutely delicious.

Stacked pumpkin muffins.

Because they stay tender and moist for days, you can make them on the weekend and still enjoy them early in the week.


One of the best things about these pumpkin cheesecake muffins is the ingredient list – common pantry items. Plus, it is a great way to use up some of the spices that sit in the pantry most of the year.

ingredients for pumpkin muffins

To make the cheesecake filling, you’ll also need cream cheese and powdered sugar.

How to make pumpkin cheesecake muffins

Making muffins is as easy as mixing wet ingredients together in one bowl and dry ingredients in a separate bowl. Pour wet ingredients into dry ingredients and stir until combined. This is called the muffin method.

Pumpkin cheesecake muffin cut in half.

First, make the cheesecake filling. Use a small cookie scoop or a spoon to form the cheesecake filling. Then place in the freezer for 15 – 20 minutes while you make the muffin batter.

Line a muffin pan with paper liners (or butter and flour the pan), then fill 1/2 full with pumpkin muffin batter. Place cheesecake balls in center of filled muffin cups.

Step by step instructions for pumpkin cheesecake muffins.

Cover with additional batter until about 2/3 full. Using a small offset spatula, smooth the tops. Sprinkle with cinnamon sugar and bake!

Don’t be shy with the cinnamon sugar topping – I used about 1/2 teaspoon on each muffin.

muffin batter

Lastly, make sure everything is room temperature before you start. Pouring melted butter into cold eggs will make it clump up and we want it to fully incorporate into a nice smooth mixture.

Muffins with small pumpkin loaf.

Normally, I use tulip muffin liners when I bake, but this time I used regular paper liners. This gave me a bit of extra batter – exactly enough for one mini loaf pan.

Pumpkin cheesecake muffin Q & A

Can I freeze these muffins?

Because of the cheesecake filling, I would not recommend freezing them.

How long do these pumpkin muffins stay fresh?

Ours lasted 4 days – until they were all eaten. They were still perfectly moist on day 4.

Why use butter and oil in the recipe?

Butter is for flavor, but it doesn’t make the moistest baked goods. That’s where vegetable or canola oil comes in – it helps to keep the muffins moist.

Can I use a silicone baking mold for these muffins?

I don’t recommend it. Silicone doesn’t brown very well and you will likely be disappointed by the results.

Baked pumpkin cheesecake muffins with cinnamon sugar.

Variations and substitutions

To give these pumpkin cheesecake muffins a crumb topping instead of cinnamon sugar, try topping the muffins with a streusel topping like these blueberry peach muffins.

To substitute the individual spices, you can use store-bought pumpkin spice mix as a short cut.

Try adding a pinch of cinnamon to the cheesecake filling for extra spice.

More pumpkin recipes to try this fall

Pumpkin cheese muffins on cooling rack.

Helpful tools and equipment

  • I use a rubber spatula to stir the batter, as it’s easier to scrape the bottom of the bowl to incorporate the flour instead of stirring with a spoon.
  • Nonstick muffin pans are perfect for those who don’t want to use paper liners.
  • If you are going to use paper liners, go straight to commercial bakeware, like this traditional muffin pan

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Pumpkin cheesecake muffins

Cheryl Bennett
Pumpkin cheesecake muffins are full of warm spices, making them the perfect fall treat.
5 from 3 votes
Prep Time 15 minutes
Cook Time 20 minutes
Additional Time 10 minutes
Total Time 45 minutes
Course Muffin recipes
Cuisine American
Servings 15 muffins
Calories 329 kcal


Cheesecake filling

  • 8 oz. cream cheese room temperature
  • 1 cup powdered sugar
  • 1 teaspoon vanilla extract

For the muffins

  • 2 cups all purpose flour 8.5 ounces by weight
  • 1 tsp. baking powder
  • 1 tsp. baking soda
  • 1/2 tsp. salt
  • 1 1/2 tsp. cinnamon
  • 1/2 tsp. ground ginger
  • 1/4 tsp. nutmeg
  • 1/4 tsp. ground cloves
  • 1 cup pumpkin purée
  • 2 eggs
  • 2 tsp. vanilla
  • 1 1/4 cup sugar
  • 8 tbsp. unsalted butter melted and cooled
  • 1/3 cup canola or vegetable oil
  • 2 1/2 tbsp. cinnamon sugar 2 tsp. cinnamon + 2 tbsp. sugar, or to taste


  • Make cheesecake filling
  • In a small bowl, whisk cream cheese, powdered sugar and vanilla together until smooth.
  • Using a mini cookie scoop or spoon, form 15 balls of cheesecake filling (or 12 if you want to make a mini loaf of pumpkin bread).
  • Place in the freezer for 15 – 20 minutes while you make the muffin batter.
  • Make the muffins
  • Preheat oven to 400°F // 200°C // Gas mark 6.
  • Line a muffin tin with papers. (Or butter and flour the pan / coat with nonstick baking spray).
  • In a medium bowl, combine flour, baking powder, baking soda, salt, cinnamon, ginger, nutmeg and cloves (*or pumpkin pie spice – see note). Whisk to combine and set aside.
  • In a small bowl, combine pumpkin purée, eggs, vanilla, sugar, melted butter and oil. Whisk to combine.
  • Pour wet ingredients over dry ingredients. Gently stir with a spatula until flour mixture is incorporated, making sure to scrape the bottom of the bowl.
  • Fill muffin liners 1/2 full. Place one cheesecake ball in the center of the half-filled muffin cup.
  • Then top with additional batter until cup is 2/3 full, smoothing the top with a small offset spatula.
  • Sprinkle each muffin with 1/2 teaspoon cinnamon sugar.
  • Bake for 18 – 20 minutes, or until a tester comes out with only a few moist crumbs attached. (Slide tester in at an angle to avoid filling)
  • Let muffins cool in tin for 10 minutes before removing to a cooling rack to cool completely.



*You can substitute 2 tsp. pumpkin pie spice for the individual spices.


Serving: 1gCalories: 329kcalCarbohydrates: 41gProtein: 4gFat: 17gSaturated Fat: 8gPolyunsaturated Fat: 8gCholesterol: 56mgSodium: 253mgFiber: 1gSugar: 27g
Tried this recipe?Let us know how it was!

Thanks for stopping by! Have a delicious day 🙂

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  1. The Print part didn’t work out well. Would have printed on several pages with mostly empty areas.

    Also do you have gluten free recipes? I would love to make this pumpkin cheesecake muffins for a gluten sensitive friend

    1. I’m sorry the print version didn’t work well. I’m not sure what happened. Can you try the recipe with GF flour? I haven’t, so I cannot say, but it would be worth a try. I do have a few GF recipes that you might like. You can search under “by diet”.

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