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.

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 little 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.

cheesecake batter and pumpkin batter

pumpkin cheesecake muffin batter in muffin pan

crumb cake topping for 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

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

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 (62g) all-purpose flour
  • 1 teaspoon ground cinnamon
  • 1/4 cup (60g) unsalted butter, melted

Pumpkin Muffins

  • 1 and 3/4 cups (220g) 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
  • 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 muffins: 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 15-16 minutes. The total time these muffins should be in the oven is around 20-22 minutes. Allow the muffins to cool for 10 minutes in the pan, then transfer to a wire rack to cool until ready to eat.
  7. Muffins taste best on the same day, though they may be covered tightly and stored 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

Pumpkin spice muffins filled with a cream cheese filling and topped with cinnamon streusel-- these are a fall favorite!


  1. Hi Sally!

    I made these muffins (let’s just call them cupcakes so they don’t sound healthy!) today and they are so perfectly fally! I used an entire 8 oz. package of cream cheese and got 19 cupcakes out of this recipe. Mine took 17-18 minutes total but probably could have been done around 15 minutes. These are so sweet and pumpkin-y and I can’t wait to make them again! The only change I made was to add oats to the crumble… I read it wasn’t setting up for some people and thought this would help. Not sure if it did anything or not but the key to the crumble is definitely making it first (as you suggest) and letting the butter harden. Then I just broke it apart with a fork and sprinkled it on top!

    I’ve also made your glazed apple cake this week! Soooo good! My glaze did not work and just soaked into the cake. It tasted great but I’m not even sure the cake needed it- it made everything a little soggy. Next on my list is your baked donuts! I’m currently pregnant and craving donuts so I think it would be cute to make this recipe for my baby shower! I will let you know how those turn out. Thanks again for your creative work! Please go on tour again and come to Cleveland, Ohio! 🙂

  2. Hi Sally! I saw this recipe yesterday and it sounded delicious so I had to try it! My muffin batter and cheesecake filling both tasted wonderful. I put the muffins in at 425 for 5 minutes and 350 for 16 minutes. While they looked great in the oven, they immediately fell down when I took them out. Is there anything I should do differently to keep them nice and tall? I think I should have left them in longer because they weren’t cooked through all the way (bottom was pretty mushy and wet) – but I think that’s just my oven being difficult. Thank you!!

    1. Hi Jen! You’re right– this usually happens when cupcakes or muffins are underbaked. I truly think baking a little extra longer will help resolve the issue.

      1. Hi Sally – Thank you for your quick response! I didn’t have time to finish last night so I left my batter and cream cheese filling in the fridge… do you think it’s still okay to use and finish up tonight?? Thank you!

  3. I made these last night! So yummy. I ate one right away, froze half and put the others in the fridge for breakfast this week. Thank you for the great recipe

  4. Well… the title of this recipe is: Pumpkin Cheesecake MUFFINS. So, I pulled out my muffin tins and proceeded with the recipe. Everything was going smoothly until the instructions say to fill each muffin with 1 tablespoon of batter, followed by 1 tablespoon of cream cheese mixture. In a muffin tin world, this would only show about 1/3 full – way far from filling to the top, as you are supposed to do. After realizing this recipe was intended for ‘cupcake’ size pans, I increased the batter/cream cheese ratio. Still had about 1/2 cup cream cheese mixture left over that I had to throw out. Wish this recipe specified using ‘cupcake’ size pans. I trust by the previous comments that they will taste fine – too hot to tell, as I just removed from the oven.

    1. sorry if this is dumb but- whats the different between muffin and cupcake pans?? i did notice after reading this that the muffins look smaller than the ones i usually make (though to be fair, i use the jumbo liners), but is there a drastic size difference? 1 tbsp/1 tbsp sounds almost like she means the mini muffin pans? im just a bit confused

  5. I want to thank you for this amazing pumpkin muffins, I just made them today for our Christmas eve dinner as dessert and I just tried one and mmmmm maybe I will hide them from the family 😉  ok, just kidding but they are amazing. Thank you! I wish I could add a picture of how they look. I made muffins and three small breads. Merry Christmas. 

  6. Sally, my teenage girls LOVE these muffins! I had originally made them in the Fall and they were deemed “okay”. In the last 2 weeks, I’ve made 6 batches; they always disappear within 2 days!! Reading your blog over the last few years has given me the confidence to experiment and now I use a combination of your pumpkin pie spices AND your chai snickerdoodle spices for the muffins. Talk about flavor!

    1. I bet those two flavors are wonderful together! And I am so so happy that you have gained confidence in the kitchen!!

  7. I just finished baking these little delights as I’ve had a major craving for pumpkin cream cheese lately.
    I used a gluten free flour and they came out perfect!!!!  Thank you for sharing this recipe! Amazing !

  8. I just made these on this beautiful fall afternoon.

    But Sally, I think you should update the title of this recipe to read “mini-cupcakes” because the batter was not able to fill more than 1 6-muffin muffin tin. So for a bit of warning: do not make this using muffin tins or you will only get 6 out of this recipe. I made more batter after realizing this.

    The muffins came out really moist, but the “dollop” of cheesecake just stayed in one place, so I think it would be better to swirl the cheesecake through with a toothpick. I added a small bit of cheesecake dollop on top and swirled through and they came out really pretty, especially with the streusal on top.

    But overall I thought the muffins didn’t taste sweet enough, and the streusal didn’t come out sweet enough. Next time I will use more sugar.

    1. I wonder how you could only get 6 muffins out of all this batter! Using a traditional muffin pan? They’re supposed to be stuffed with cheesecake, not stirred though you can absolutely swirl it in if you prefer. Yum! Thanks for trying them!

  9. Hello, I was wondering: ou have a recipe for Pumpkin Pie Spice (Cinnamon, Clove, Nutmeg, Ginger, All-Spice) but in this Recipe you do not recommend to ad the Ginger (only Clove, Nutmeg and Allspice) and the cinnamon content is higher compared to the Mixture. I have never used Pumpkin Pie Spice before… What is better? Thank you very much for your advice!!

      1. Thank you very much! I love cinnamon too! For this muffins I would like to use the Pimpkin spice mixture with the 5 Ingredients and ad more cinnamon- what would be the right amount? Like 2 teaspoons mixture and 1 spoon extra cinnamon?

  10. Hi Sally, I have everything to make these except for the liners do I really need to use them. and if I don’t could I just pray the muffin tins ordo I need to butter and flour. I loved your apple bread I added nuts to some of the loaves and not all the loaves got the glaze and both ways were a hit. Thanks for sharing with us.. LOL

  11. Made these this evening. Ended up with 16 made in silicone muffin cups. Used all pumpkin spice mix instead of part cinnamon part spice mix. Added some pumpkin seeds to the struesel topping. Refrigerated cream cheese mix and the struesel topping, used a small 1tbsp scoop to drop a dollop in the middle of the batter. Refrigerating the topping made it easier to crumble on the top. Loved the way the high temp at the beginning gave them a nice high domed top. These will definitely become part of my fall recipe rotation. Thanks for the great recipe!

  12. 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 😉

  13. I’m concerned about them not being refrigerated, I left them out and covered overnight forgetting to refrigerate them and I was so worried I would have to throw them out but I see your reciysays they can sit out for 3 days even with the cheese filling.

    1. Hi Amy! That’s my suggestion, but please use your best judgement and if you’d like to refrigerate them, by all means– you can! 🙂

  14. I love the recipe! However I found it not to be a 25 minute prep time and the amount of batter made barely enough for 12. Thank you for the delicious new recipe to add to my collection.

  15. 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!!

  16. I cant wait to try this wonderful recipe. I layered the batter and cheesecake filling into a casserole dish and am wondering how long and at what temp would be best to bake it?
    Thank you!

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I’m Sally, a cookbook author, photographer, and blogger. My goal is to give you the confidence and knowledge to cook and bake from scratch while providing quality recipes and plenty of pictures. Grab a cookie, take a seat, and have fun exploring! more about Sally