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Like a delicious pumpkin roll, these pumpkin cream cheese muffins combine perfectly spiced pumpkin muffins with cream cheese filling. Top the muffins with brown sugar crumb cake topping and you have an absolutely irresistible pumpkin spice breakfast treat.

stack of pumpkin cheesecake muffins

It’s time to cross something off your fall to-do list: make the best pumpkin muffins!

Every year when the weather begins to cool down, I suddenly begin craving all of the season’s comforting flavors. I’m pretty sure I’m not alone here– a pumpkin-spice alarm goes off in all our brains. One of the first recipes with pumpkin I prepare each year are these pumpkin cheesecake muffins. I originally published this recipe in 2013 and it’s been a fall favorite since!

Everything to Love About Pumpkin Cheesecake Muffins

plate of pumpkin cheesecake muffins

3 Parts to Pumpkin Cream Cheese Muffins

  1. Pumpkin Muffins: There’s many different ways to prepare pumpkin muffins. You could leave these muffins completely plain without the cream cheese filling and crumb cake topping, and you’ll have a mildly sweet muffin. I keep the sugar on the lower side since there’s sugar in the filling and crumb topping. When I make plain muffins, I usually make my pumpkin crumb cake muffins instead. Or even these mini cinnamon sugar pumpkin muffins, which taste like the miniature version of pumpkin donuts!
  2. Cheesecake Filling: You need 4 simple ingredients for the cream cheese filling. Bring some block cream cheese to room temperature, then beat it with 1 egg yolk, sugar, and a touch of vanilla extract. The egg yolk helps the cream cheese filling “set” like cheesecake.
  3. Crumb Topping: You also need 4 ingredients for the crumb topping including flour, melted butter, brown sugar, and cinnamon. Make the crumb topping first so it’s ready.

You need 4 mixing bowls: 1 for the muffin’s dry ingredients, 1 for the muffin’s wet ingredients, 1 for the cheesecake filling, and 1 for the crumb cake topping.

2 images of batter for pumpkin cheesecake muffins
pumpkin cheesecake muffin batter in muffin pan
2 images of crumb cake topping in a bowl and sprinkled onto pumpkin cheesecake muffins

Overview: How to Make Pumpkin Cream Cheese Muffins

  1. Prepare crumb cake topping.
  2. Prepare pumpkin muffin batter. Use a whisk to bring all the ingredients together.
  3. Prepare cheesecake filling. You need a mixer for this step.
  4. Layer the pumpkin batter and cheesecake filling together.
  5. Add crumb cake topping. Press it down into the tops of each muffin so it sticks.
  6. Bake. Your kitchen will smell like a pumpkin spice candle!
pumpkin cheesecake muffins on a plate

Which part of these pumpkin cheesecake muffins will you like best? I’m not sure I can play favorites! There’s just so much to love because every layer has a different texture and taste. A moist and flavor-packed tender pumpkin muffin, generously spiced and lightly sweetened with brown sugar. The cheesecake is a tangy, yet sweet ripple of creamy goodness. And the buttery slightly crunchy crumbles on top add the perfect finishing touch.

pumpkin muffin filled with cream cheese and topped with crumb

More Pumpkin Baking Recipes

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stack of pumpkin cheesecake muffins

Pumpkin Cream Cheese Muffins

  • Author: Sally
  • Prep Time: 25 minutes
  • Cook Time: 22 minutes
  • Total Time: 50 minutes
  • Yield: 1214 muffins 1x
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American


Like a delicious pumpkin roll, these pumpkin cream cheese muffins combine perfectly spiced pumpkin muffins with cream cheese filling. Top the muffins with brown sugar crumb cake topping and you have an absolutely irresistible pumpkin spice breakfast treat.



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*
  • 3/4 cup (150g) 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


  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.

Keywords: pumpkin, cream cheese, breakfast

Reader Questions and Reviews

    1. Hi Vicki, pumpkin pie filling contains extra ingredients and sweeteners and is also a different consistency than pumpkin puree. It’s best to wait until you can purchase pumpkin puree, otherwise the taste and texture will be compromised.

  1. Hi Sally,
    I made this recipe and it came out exactly like those pictures above, the only thing that I would change is the sweetness of the cupcake itself. I would increase the amount of sugar a bit more.
    I will absolutely make these again. Thanks for sharing this recipe.
    – Ariel

    1. I wish I had read this before I baked them because I think they need a bit more sweetness too. I think I’ll add a glaze to mine.

    1. Hi Luke, for absolute best results, we recommend sticking with oil in this recipe.

  2. Could I use softened butter instead of melted butter for crumb topping? ( like on a crumb top apple pie?)
    Btw; so far I’ve loved all the recipes I’ve tried from you! Thank you so much!!

    1. Hi Joann, I wouldn’t use softened butter because that could create more of a paste than a crumble. You could try using cold and cubed butter and cut it in using a pastry cutter though. (That’s how we make the topping for Pumpkin French Toast Casserole.)

  3. Is it possible to use jumbo muffins cups? If so, approximately the baking time?

    1. Absolutely! We recommend a 9×5 inch loaf pan. The bake time will be longer. Use a toothpick to test for doneness.

  4. These were exactly what my Halloween morning needed! My first reaction was that they weren’t too sweet. Great balance of the cheesecake and pumpkin. I used buttermilk to get a moister muffin.

    While I did use canned pumpkin puree, I wanted to know if using fresh pumpkin does the recipe need any modification? I much prefer roasting and pureeing pumpkins this time of year.

    1. Hi Lori, you can use fresh puree here with no other changes needed. So glad you enjoyed these muffins!

  5. I absolutely love all of Sally’s recipes, they are the only ones that I use for baking. This one absolutely hit it out of the park, I have had such positive feedback leaving everyone wanting more when I made these muffins!!! Highly recommend making these coming from a baker!!!

  6. I’ve made these muffins a few times now and every batch has come out great! Always a family favourite. Do you think this recipe would work if I wanted to make mini muffins?

    1. Hi Pav, definitely! For mini muffins, bake at 350 degrees (the entire time) for about 12-14 minutes, give or take. Keep a close eye on them and use a toothpick to test for doneness.

  7. This was the first recipe I made from this site. Just made these again and they’re incredible. This time I did add the maple glaze from your maple cinnamon roll recipe. Takes some time to make these, but worth it! Next time I’ll try it in a 9×5 loaf pan. Thanks for so many great recipes!

  8. Hi Sally,
    Could I add oats to this recipe to make it more of a breakfast-y muffin? If so, how much would you recommend? Would you reduce the amount of flour?

    Thank you so much!

  9. Hello Sally,

    I recently made the Blueberry Muffins with the walnut brown sugar topping. Those were a 12/10 btw!!! It got me thinking about the fall and how a pumpkin muffin would be good, and of course you had a recipe for it! I felt like the walnuts were a huge success in the blueberry muffins and wanted to know if I could add chopped pecans to the topping of this pumpkin cream cheese muffin, or if you think that would mess up the recipe.

    Thank you,

    Will be trying this come fall! Your blueberry muffins were, “FIRE”!!! I looked through quite a few blueberry muffin recipes and after reading a few I knew yours were the best on the internet.

    Mike C

    1. Hi Mike, we can’t see why not! Nuts would be a delicious addition to the topping. Let us know how it goes and thanks so much for making and trusting our recipes!

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