Pumpkin Cheesecake Muffins

Like a delicious pumpkin roll, these pumpkin cheesecake 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!

Everything to Love About Pumpkin Cheesecake Muffins

  • Tastes like dessert for breakfast
  • Crave-worthy pumpkin spice flavor
  • Lightly sweetened cheesecake filling
  • Easy to transport & share
  • Stay moist & soft for days
  • Like pumpkin coffee cake and pumpkin swirl cheesecake in 1!!

plate of pumpkin cheesecake muffins

3 Parts to Pumpkin Cheesecake 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

How to Make Pumpkin Cheesecake 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.

And can I just add that my husband doesn’t even like pumpkin and he devours these. Literally no one can resist crumb topping.

pumpkin cheesecake muffin

More Pumpkin Baking Recipes

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stack of pumpkin cheesecake muffins

Pumpkin Cheesecake Muffins

  • Author: Sally
  • Prep Time: 25 minutes
  • Cook Time: 22 minutes
  • Total Time: 50 minutes
  • Yield: 12-14 muffins
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American


Like a delicious pumpkin roll, these pumpkin cheesecake 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*
  • 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

Cheesecake 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


  1. Made these with 3/4 cup of whole wheat flour (remaining was all purpose) just to make them a weeee bit healthy. For muffins these are awesome! Love the variety of textures, and flavors going on, and they are not too sweet (sometimes muffins are more like cupcakes to me!) Saving this recipe for sure! Thanks for the great instructions as well, even though this required many bowls 😉

  2. These are amazing!! I’ve made several of your “sweet” recipes over the past couple of weeks for my boyfriend to bring in to work and they have loved everything so far. I just made this one today and they are the best ones yet. I can’t wait to try more of your recipes!! Thank you for sharing!!

  3. Could you make this in a bread loaf pan?

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

  4. Loved these! My husband loves pumpkin pie and I just made these for his birthday on the 12th and he LOVED them! Thank you for so many amazing recipes! I’ve made the honey garlic shrimp quite a few times and everyone loves that too! The one problem I had was I didnt use muffin liners and a few of the top half of the muffins came off after cooling…. they still tasted amazing and my house smelled amazing while they were cooking! I have a heart shaped donut baking pan and did a few in that with just small dollops of cheesecake batter stuffed around them and baked them for about 16-20 minutes at the lower temp and they turned out amazing! Again thanks for all of the amazing recipes, everyone loves everything that I make that comes from you!

  5. I made these today for visiting kids and grands. Loved by all. Thank you for the wonderful recipes.

  6. This recipe is delicious! I followed the instructions and they turned out great. Thank you for sharing!

  7. I made these on the weekend and they are amazing! They’re a perfect fall breakfast treat. Thanks Sally!

  8. Made these over the weekend. I think I maybe underfilled a little, since I got more like 18 muffins, but they were delicious! Even my sister who HATES pumpkin declared them almost good enough to pay for. Definitely a keeper recipe. But what do I do with the leftover canned pumpkin?

    1. Hi Betsey! I have so many other pumpkin recipes! I hope you find one to try next. https://sallysbakingaddiction.com/tag/pumpkin/

  9. I don’t love pumpkin but these were great! I brought them to work and everyone loved the pumpkin cheesecake muffins. Thank you, Sally!

  10. These turned out perfectly! I knew I would love them as soon as I saw the title. How can you go wrong?
    I actually prefer a less sweet muffin so I was generous with the spices and did not pack the brown sugar. I followed the directions and they turned out perfectly. Thanks very much Sally, I love your recipes and this one is another winner!

  11. Hi Sally,
    I wanted to make these muffins but use your pumpkin cupcake recipe as well as the cream cheese frosting. Would you recommend baking the cupcakes the same amount of time as the muffin recipe or the cupcake recipe since I will be putting in the cheesecake? Or do you think this combination won’t work out haha:) Thanks!

    1. Hi Liz! If I’m understanding correctly, you’re asking to bake the cream cheese frosting in the cupcakes? I don’t recommend that. Use this cheesecake filling and my pumpkin cupcake batter (or this muffin batter). Bake according to the muffin instructions.

  12. Super good recipe the muffins tasted so good! My only question is how could you keep the cream cheese filling from coming out like lava! All(or most) came out from the tops. Otherwise super good.

  13. Yum! I got 12 beautiful muffins out of this recipe. They are tall and puffy and absolutely perfect! Also, very delicious! That crumb on top is so good! Thanks Sally, your recipes always turn out amazing!

  14. My favorite fall muffin recipe! The only thing I changed was adding grated orange zest to the cheesecake filling!

  15. Loved these every time!
    I was impatient when making these last time, and couldn’t wait to chill the cream cheese filling. I put it into a heavy duty Ziploc baggie, snipped off a corner and squirted a “dollop” into each (exactly where and how much as stated in your recipe). I used my kitchen scissors to cut off the dollop. It was fast and easy!

  16. Hi, Sally! L❤VE your site.
    I have some leftover cream cheese fristing from baking a carrot cake. Think I could just add an egg (in equal proportions to recipe) to it for the filling?

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Liz, The frosting is made with both butter and a lot more confectioners sugar than the granulated sugar here, so it does have a very different consistency and taste than this filling. You can certainly try it but the results will be different.

  17. Do you think these would work in a jumbo muffin form? Thank you so much for all your amazing recipes !

    1. Stephanie @ Sally's Baking Addiction says:

      Hi Jennifer, Yes this will work as jumbo muffins! I’m unsure of the exact bake time needed.

  18. These were perfection! For anyone else who is GLUTEN FREE, please know that this recipe came out terrific. I used a 1:1 GF flour (like Bob’s Red Mill) and used the weight measurements. You MUST weigh. I put 62g in the crumb topping and 220g in the muffin batter. Followed all of Sally’s instructions and other measurements to the letter. A must bake for fall!

    PS: I did get a 14-muffin yield with GF flour.

  19. I used paper muffin cups and the bottom layer stuck to the muffin and the muffins were very dry. I followed the recipe exactly so not sure what happened.

  20. Camille Adele says:

    Hi Sally! These muffins were absolutely delicious. I love the cheesecake part of it (it evens out the pumpkin flavor with a hint of sweetness!), and I am so glad that I found the recipe. I like to add extra crumb topping, because I absolutely love crumb toppings (!) and it tastes amazing. 5 stars from me!

  21. Made these for a friend, and we both agreed it’s a keeper-recipe! Super moist, not too sweet and great fall flavor. I got 14 perfect muffins out of the batter.

  22. Absolutely delicious!!!

  23. Can these be made with mascarpone instead of the cream cheese?

    1. I can’t see why not.

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