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Pumpkin Spice Cheesecake Muffins

I found myself (yet again) having two events in one day that I needed to bake for, but had such little time. It was also October, my favorite month of the year, and I really wanted to incorporate pumpkin into a baked dessert. I love working with all the warm flavors of October like chai, apple, and cinnamon, but I've never actually baked with pumpkin before. I decided it was time to embrace my inner fall basic b*tch, and get on this pumpkin train.

I began my search, and was pretty overwhelmed trying to decide on what to bake (because I wanted to try ALL the amazing fall desserts out there). Since I was bringing it to two separate places, I knew I wanted to do something like a cupcake, muffin, or cookies--something that I could easily divide up and carry with me to multiple destinations.

I ended up once again on my all-time favorite recipe website Sally's Baking Addiction. This website is like a treasure trove of all things baked goods. I know I've mentioned this website before in a different post, but I cannot express enough how incredible her desserts are, and also how easy the recipes are to follow.

I was torn between her regular pumpkin muffins and these beauties. I'm a sucker for a cheesecake filling, and I love a good challenge, so these were the winner. They were actually much easier to make than I thought they would be. All you have to do is make each part correctly, then put it all together. It makes about 12-14 muffins, so I was able to split them up and take them to each of my events. They were a huge hit!

These muffins are one part pumpkin muffin and one part cheesecake filling, topped with a wonderful brown sugar cinnamon crumble. The result is a luscious, soft muffin, with a delectable, smooth cheesecake filling that greatly compliments the pumpkin and cinnamon flavor. The crumble adds lots of texture and more warm notes of cinnamon and brown sugar. These muffins are a very delicious autumn treat!

Here's What You Need:

Crumb Topping
  • 1/4 cup (50g) packed light or dark brown sugar

  • 1/2 cup (63g) all-purpose flour

  • 1 teaspoon ground cinnamon

  • 1/4 cup (60g) unsalted butter, melted

Pumpkin Muffins
  • 1 and 3/4 cups (219g) all-purpose flour (spoon & leveled)

  • 1 teaspoon baking powder

  • 1 teaspoon baking soda

  • 1/2 teaspoon salt

  • 1 and 1/2 teaspoons ground cinnamon

  • 1 teaspoon pumpkin pie spice*

  • 2/3 cup (133g) packed light or dark brown sugar

  • 2 large eggs, at room temperature

  • 1 cup (227g) canned pumpkin puree

  • 1/2 cup (120ml) vegetable oil (or melted coconut oil)

  • 1/3 cup (80ml) milk

  • 1 teaspoon pure vanilla extract

Cream Cheese Filling
  • 6 ounces (168g) block cream cheese, softened to room temperature

  • 1 egg yolk, at room temperature

  • 1/2 teaspoon pure vanilla extract

  • 3 Tablespoons (36g) granulated sugar

Here's What To Do:

  1. Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners. This recipe makes 12-14 muffins, so you may need a 2nd muffin pan or bake this recipe in batches.

  2. Make the crumb-topping first: Combine the brown sugar, flour, and cinnamon in a small bowl and mix until combined. Add the melted butter and gently mix with a fork until crumbs form. Don’t over-mix into a paste. Just mix until it is crumbly. Set aside.

  3. Make the pumpkin batter: Whisk the flour, baking powder, baking soda, salt, cinnamon and pumpkin pie spice together in a large bowl. Set aside. In a medium bowl, whisk the brown sugar, eggs, pumpkin, oil, milk, and vanilla extract together. Pour the wet ingredients into the dry ingredients and whisk or stir until just combined. Avoid over-mixing.

  4. Make the cheesecake filling: Using a handheld or stand mixer fitted with a paddle or whisk attachment, beat the cream cheese in a medium bowl on medium-high speed until smooth and creamy. Beat in the egg yolk, vanilla extract, and sugar until combined.

  5. Spoon 1 heaping Tablespoon of pumpkin muffin batter into the muffin cups. Layer with about 1 spoonful (not quite a full Tablespoon) of cheesecake filling, then another heaping Tablespoon of muffin batter– or however much batter is needed to fill the cups all the way to the top. Some cheesecake filling may poke out of the top or on the sides. Sprinkle crumb topping onto each, then press it down into the tops of the muffins to help prevent it from falling off as the muffins bake.

  6. Bake for 5 minutes 425°F (218°C) then, keeping the muffins in the oven, reduce heat to 350°F (177°C)* and continue baking for another 15-17 minutes. The total time these muffins should be in the oven is around 20-22 minutes. Allow to cool for at least 10 minutes in the pan before serving.

  7. Cover leftover muffins tightly and store at room temperature for up to 2 days or in the refrigerator for up to 1 week.


  1. Freezing Instructions: For longer storage, freeze the muffins for up to 3 months. Thaw overnight in the refrigerator, then heat up in the microwave if desired.

  2. Pumpkin Pie Spice: Instead of the pumpkin pie spice, you can use 1/4 teaspoon ground cloves, 1/2 teaspoon ground allspice, and 1/4 teaspoon ground nutmeg.

  3. Why the initial high oven temperature? Like I do for most muffin recipes, bake the muffins for 5 minutes at a very hot temperature. Then, keeping the muffins in the oven, switch to a lower temperature for the remaining bake time. This initial high temperature will quickly lift the muffin tops so they’re extra high, then the centers will bake during the lower temperature bake time. This trick makes beautiful bakery-style muffins every time.


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