Pumpkin Cheesecake Swirl Cupcakes with Walnut Crumble from Scratch

Pumpkin Cheesecake Swirl Cupcakes with Walnut Crumble from Scratch

Your favorite autumn treats are here: moist, yet light Spiced Pumpkin Cheesecake Cupcakes with Walnut Crumble. They are not your regular cupcakes as they are covered with a delicious cheesecake swirl which then in turn is topped with crunchy walnut crumble. Make them before or after Halloween, they taste divine in any occasion. Even if you don’t have pumpkin puree or pumpkin spice at hand or on sale in stores nearby you, I will take you through how to make these babies from scratch in an easy how-to.

Mari Bakes pumpkin cupcakes

Growing up in northeastern Europe, pumpkins were traditionally only used for savory dishes. The whole American craze for pumpkin pies and pumpkin cheesecakes totally missed us. My grandfather did make killer pickled pumpkins though, which were served at every Christmas dinner. Nevertheless, when I saw pumpkins at our local farmer’s market here in the Netherlands, I knew I wanted to try making something sweet out of them. 

First up, I thought I’d bake something simple, so I chose Pumpkin Cupcakes! But with lots of toppings because we all deserve that bit of extra. And boy, did they make me understand the pumpkin dessert fanaticism! 

These cupcakes come together in a jiffy…unless you live in northeastern/northwestern Europe and need to make the pumpkin puree and pumpkin spice from scratch like me. No worries though, I got you covered on how to make both pumpkin puree and pumpkin spice easy from scratch!


How to Make Pumpkin Puree from Scratch

Following one of my favorite food bloggers Minimalist Baker, to make your own pumpkin puree, preheat your oven to 175 degrees. Then, cut your beautiful pumpkin in half and scoop out the seeds and the stringy bits. Brush the inside with some oil (I used coconut oil but other oils such as olive, avocado, etc., work as well). Sprinkle a pinch of salt on the inside and put it flesh down on a baking paper on the baking sheet. Pierce the skin a few times with a fork to help it bake better. Let it do it’s thing in the oven for 40-50 minutes, depending on the size of your pumpkin. When it is baked, it will be soft, mushy and slightly caramelized from the bottom. Let it cool for around 15 minutes and then scoop out the fleshy part. Transfer it into a kitchen machine or blender and whiz it until the puree is nice and smooth in consistency.

roasted pumpkins

Mari Bakes pumpkin puree


How to Make Pumpkin Spice Blend

Spoiler alert, there’s no pumpkin included in the spice mix. The term pumpkin spice comes from spices traditionally used for pumpkin pie. Making your own pumpkin spice blend is easy!

Mix together:

  • 3 tbsp ground cinnamon
  • 3 tsp ground ginger
  • 1 tsp ground cloves
  • 1 tsp ground nutmeg
  • 1/2 tsp ground allspice

    Mari Bakes pumpkin spice


Now, time for the real deal!

Mari Bakes pumpkin cupcakes

Pumpkin Cheesecake Swirl Cupcakes with Walnut Crumble

These Pumpkin Cheesecake Swirl Cupcakes are moist, light and autumnal, covered in a delicious cheesecake swirl and topped with a crunchy walnut crumble. They are guaranteed to vanish from your table. Luckily this recipe makes enough so you might be lucky and also grab some leftovers.
Prep Time 15 minutes
Cook Time 22 minutes
Course Dessert
Cuisine American
Servings 22 cupcakes


Pumpkin Cupcake

  • 150 grams all purpose flour* (see notes)
  • 80 grams whole-wheat flour*
  • 1 tbsp pumpkin spice (see recipe above)
  • 1 tsp baking soda
  • ½ tsp salt
  • 400 g pumpkin puree (see recipe above)
  • 1 cup brown sugar
  • ¼ cup maple syrup
  • 2 eggs
  • ½ cup vegetable oil (neutral tasting one, e.g. sunflower oil)
  • 1 tsp vanilla extract

Cheesecake Swirl

  • 200 g full fat cream cheese
  • ¼ cup sugar
  • 1 egg yolk
  • 1 tsp vanilla extract

Walnut Crumble (optional)

  • 3 tbsp brown sugar
  • 3 tbsp flour (I used whole-wheat flour)
  • 2 tbsp chopped walnuts
  • 1 ½ tbsp oil (neutral tasting one, e.g. sunflower oil)
  • 1 big pinch pumpkin spice


  • Preheat the oven to 190°C (170°C fan). Fill your muffin tins with paper muffin cups. This recipe will make around 22 medium muffins. My muffin tin has 12 cups as seen on the pictures.
  • Mix the first five dry ingredients (all purpose flour, whole-wheat flour, pumpkin spice, baking soda and salt) together in a bowl.
  • In a bigger bowl, whisk together pumpkin, brown sugar and maple syrup. Add in eggs, vegetable oil and vanilla extract. Mix well.
  • Slowly add the dry ingredients to the pumpkin mixture and mix until just combined and no more dry flour is visible. Do not overmix.
  • Use around 1 tablespoon of batter to fill the muffin cups about ¾ full. Adjust if using bigger or smaller muffin tins.
  • In another bowl, mix cream cheese until soft. Stir in sugar, egg yolk and vanilla extract and beat until smooth.
  • Top each muffin with a teaspoon of cheesecake mixture. Use a toothpick to swirl the cheesecake mixture into the muffin batter.
    Mari Bakes pumpkin cupcakes
  • Optional: Make the walnut crumble by combining brown sugar, chopped walnuts, flour, oil and pumpkin spice. The crumble should form little clumps but still be crumbly (as the name suggests). Top the cupcakes with a teaspoon of the walnut crumble.
    Mari Bakes pumpkin cupcakes
  • Bake for 18-22 minutes or until the tops are slightly browned and a toothpick inserted to the middle of the cupcake comes out clean.
    Mari Bakes pumpkin cupcakes
  • Let cool for a few minutes in the muffin tin and then transfer to a cooling rack to cool completely.
    Mari Bakes pumpkin cupcakes
  • When completely cooled, the cupcakes can be stored in the fridge in an air-tight box for 3 to 5 days.


*As you see, I managed to sneak in some whole-wheat flour again. You can also just go ahead and only use 230g of all purpose flour.
**For some reason, my cat went completely wild every time he got a whiff of these cupcakes! So make sure to keep your muffins safe from wild predators. 😉 
Mari Bakes pumpkin cupcakes
Keyword cheesecake, cupcakes, pumpkin

This recipe was inspired by an old Minimalist Baker and Novice Chef Blog pumpkin cupcake recipe.


I would love to know how it turned out for you! Leave a comment below, Pin it or share a picture on Instagram by tagging @maribakesbymari.

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