Pumpkin Cheesecake Muffins.

Super-moist pumpkin spice muffins stuffed with cheesecake filling and topped with brown sugar cinnamon streusel.

Pumpkin muffins filled with cream cheese filling and topped with sweet cinnamon brown sugar streusel!

It’s finally starting to look and feel like fall around here. We had a few really chilly days in September, and then a 90F degree day in October (seriously?!), and now we’re into fuzzy slipper and cute boot weather. Surely you get excited about fall just to break out your boots again, right?

I spent this past weekend crossing some things off my fall to-do list. I went out for pumpkin beers, bought a couple pumpkins to carve, stocked my fridge with locally grown Honey Crisp apples (and umm… they’re almost already gone), and we took Jude for a long walk at Centennial Park.

Seriously, look at this view:

Walk w Jude

To round out my super spirited October weekend, I made a couple test batches of pumpkin muffins. Stuffed with cheesecake and topped with streusel. Because what’s a muffin without some streusel?

They’re like a pumpkin roll turned into a muffin. Or an inside out cream cheese-frosted pumpkin bar. Cheesecake meets pumpkin pie meets crumb cake.

Pumpkin muffins filled with cream cheese filling and topped with sweet cinnamon brown sugar streusel!

There will be a lot of little bowls happening on your counter when you make today’s muffins. Sadly, that means more dishes to wash. But do extra dishes even matter when the end result is this?!

There are three parts to today’s recipe.

(1) Super-moist spiced pumpkin muffins.

(2) 4 ingredient cheesecake filling.

(3) Easy brown sugar streusel.

Let’s start with the muffins. The muffins themselves are lightly sweetened with brown sugar and left moist from pumpkin puree, oil, and eggs. You’ve actually seen them before on my website. I used this muffin batter to make cupcakes a couple months ago. With the addition of dark chocolate frosting and chocolate chips, my pumpkin muffin batter was seriously dessert-i-fied. You might want to check them out.

Pumpkin cupcakes vs pumpkin muffins. Where do you draw the line? I really don’t care where the line is between the two, especially if dark chocolate frosting or cheesecake filling are involved. Moving along…

Pumpkin muffins filled with cream cheese filling and topped with sweet cinnamon brown sugar streusel!

Next – the cheesecake filling. Oh baby. This stuff is good. You’ll only need four little ingredients: cream cheese, sugar, vanilla, and 1 egg yolk. I found that when I used an entire egg for this filling, it tasted eggy. Like cream cheese scrambled eggs. No thanks. Make sure you just use the yolk. You’ll layer the muffin batter and the cheesecake filling into the muffin liners. 1 layer muffin batter, 1 layer cheesecake, 1 layer muffin batter. It’s ok if some of your cheesecake filling is visible on the top or on the sides. That’s how you get pretty cheesecake swirls peeking out all over.

Finally? The streusel. The streusel is simple: brown sugar, flour, cinnamon, and melted butter. Sprinkle the buttery brown sugar streusel on top of the muffins before going into the oven. You’ll want to gently press it down into the batter so it won’t fall off the sides as the muffins are rising.

Pumpkin muffins filled with cream cheese filling and topped with sweet cinnamon brown sugar streusel!

I’m still not sure which part of the muffin I like the best. There’s just so much to love; every layer has a different texture and taste. A moist and flavor-packed tender pumpkin muffin, generously spiced and lightly sweetened with brown sugar. And the cheesecake! Tangy, yet sweet ripple of creamy goodness. Mmm. Oh! And the buttery slightly crunchy crumbles on top make the perfect finishing touch. I could eat the streusel with a spoon and be content. I just can’t choose. I want it all.

They pair wonderfully with a steamy cup o’ joe, make an excellent 4pm snack, and are perfectly acceptable to squeeze in right before midnight.

It may look like a lot of little ingredients, but most of them are repeated throughout each layer. Start baking!

Follow me on Instagram and tag #sallysbakingaddiction so I can see all the SBA recipes you make. 

Pumpkin Cheesecake Muffins

Yield: 14 muffins

Prep Time: 25 minutes

Total Time: 45 minutes, plus cooling

Print Recipe

Super-moist spiced pumpkin muffins stuffed with cheesecake filling and topped with brown sugar cinnamon streusel.


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 (measured correctly)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 and 1/2 teaspoons ground cinnamon
  • 1 teaspoon pumpkin pie spice1
  • 2/3 cup (133g) packed light or dark brown sugar2
  • 2 large eggs
  • 1 cup (227g) pumpkin puree
  • 1/2 cup (120ml) vegetable oil (or canola, or melted coconut oil)
  • 1/3 cup (80ml) milk
  • 1 teaspoon vanilla extract

Cheesecake Filling

  • 6 ounces (168g) cream cheese, softened to room temperature
  • 1 egg yolk
  • 1 teaspoon vanilla extract
  • 3 Tablespoons (36g) granulated sugar


  1. Preheat oven to 425°F (218°C). Line two muffin sheets with 14 liners or spray with non-stick spray. Set aside.
  2. Make the crumb-topping first: Add the brown sugar, flour, and cinnamon to a small bowl and mix until combined. Add the melted butter and mix until crumbs form. Set aside.
  3. Make the pumpkin muffins: In a large bowl, toss the flour, baking powder, baking soda, salt, cinnamon and pumpkin pie spice together until combined. Set aside. In a medium bowl, whisk the brown sugar and eggs together until combined. Whisk in the pumpkin, oil, milk, and vanilla. Pour the wet ingredients into the dry ingredients and stir until just combined. Do NOT overmix the batter.
  4. Make the cheesecake filling: In a medium bowl, beat the cream cheese with an electric handheld (or stand) mixer on medium-high speed until creamy. Add the egg yolk, vanilla extract, and sugar. Beat until combined.
  5. Spoon 1 Tablespoon of pumpkin muffin batter into the muffin cups. Layer with about 1 spoonful (not quite a full Tablespoon) of cheesecake filling, then another Tablespoon of muffin batter (or however much batter is needed to fill the cups all the way to the top). Yes, you will fill the muffin cups to the very top. Some cheesecake filling may poke out of the top or on the sides. Sprinkle each muffin evenly with crumb topping and press the topping down into the muffin so it sticks.
  6. Bake for 5 minutes 425°F (218°C) then, keeping the muffins in the oven, reduce heat to 350°F (177°C)3 and continue baking for another 15-16 minutes. The total time these muffins should be in the oven is around 20-21 minutes. Allow the muffins to cool for 10 minutes in the muffin sheet, then transfer to a wire rack to cool until ready to eat. Muffins taste best on the same day, though they may be stored covered tightly at room temperature for 3 days or in the refrigerator for 5 days.
  7. Make ahead tip: For longer storage, freeze muffins for up to 3 months. Allow to thaw overnight in the refrigerator and heat up in the microwave if desired.

Additional Notes:

  1. 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.
  2. I usually only use 1/2 cup brown sugar, but I find the pumpkin and spice flavor really excels with just a little more brown sugar. So, I prefer 2/3 cup.
  3. Why the initial high temperature? Like I do for most of my muffin recipes, you’ll 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, then the centers will bake during the lower temperature bake time.

© Sally’s Baking Addiction. All images & content are copyright protected. Please do not use my images without prior permission. If you want to republish this recipe, please re-write the recipe in your own words, or link back to this post for the recipe.

After you make these muffins, try these similar recipes next…

Cinnamon-Swirl Chocolate Chip Bread

Cinnamon-Swirl Chocolate Chip Bread

Favorite Pumpkin Oatmeal Cookies (soft, not cakey!)

These are my favorite pumpkin cookies! Filled with oats, chocolate, and cranberries!

Mini Cinnamon-Sugar Pumpkin Muffins

Mini Pumpkin Muffins

See more muffin recipes.

See more pumpkin recipes.

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

207 Responses to “Pumpkin Cheesecake Muffins.”

  1. #
    TIFposted September 30, 2015 at 6:51 am

    I am making these for the second time this week.  I am IN LOVE.  Thanks for such a great recipe that is delicious and fairly easy (even for me).  


  2. #
    Morganposted October 18, 2015 at 1:59 pm

    Made these yesterday and they were a huge hit! So delicious!! 


  3. #
    Alissaposted October 26, 2015 at 6:57 pm

    I love this recipe! Have made it twice! Although for some reason I cannot get the crumbly topping to turn out right. I’ve tried melted butter and room temperature butter and it never makes crumbs for me! Both times it was liquidy (room temp butter it was more like a spread). Any tips? 


    • Sallyreplied on October 27th, 2015 at 6:48 am

      Alissa, are you using regular all-purpose flour or something else? Because the flour is what helps the streusel keep its shape. Try adding a little more next time.


      • Alissareplied on October 27th, 2015 at 11:32 am

        Hi Sally, thanks for the quick reply! I am using regular all-purpose flour. The first time around I tried adding new more flour (I think almost double!)  and it helped a little but I still didn’t achieve a crumb consistency. I am weighing all ingredients too so the measurements should be accurate. Maybe I’ll try adding even more flour. I was using a fork to try to mix everything together. Should I try a spoon? 

    • Jaymereplied on November 11th, 2015 at 10:59 pm

      I’m not sure if you will see this, but mine did the exact same thing! Came out like a liquid. I just kept adding flour, brown sugar and cinnamon until it turned into a crumb! It tastes perfect! 


    • Rachel Schifferreplied on August 23rd, 2016 at 12:44 pm

      Do not  melt the butter!  Use softened butter and then blend the ingredients with your hands and it will turn out like crumble topping for berry crisp.


  4. #
    Bevposted October 29, 2015 at 7:56 am

    O.M.G. These are the most delicious pumpkin muffins I’ve made so far!! My husband has been raving about them for the past two days. (I don’t think there’s any left!) Though slightly complicated, what with the three bowls and assembling, I managed to bake them and was amazed that they rose, considering I was mixing and measuring with my 4yr old grandson who was stealing bits of sugar.   That grandson actually contributed to the recipe-I had peeled a whole banana for him at breakfast which he saw a brown spot on and promptly refused to eat, so I switched the banana for the oil and the muffins were still moist.  I also replaced 3/4 c of flour with whole wheat flour (in an attempt to label the muffins “healthy”) and they still managed to rise! 
    Thank you Sally for these yummy recipes! 


  5. #
    Sarahposted November 1, 2015 at 10:24 am

    Made these cupckakes and they turned out great! Was thinking about making an 8″ round cake like this.  Cooking time suggestions? 


    • Sallyreplied on November 2nd, 2015 at 8:51 am

      I’m really unsure. Over 30 minutes for sure. Make sure you use a deep dish cake pan or even a springform pan with high sides. This will be a very thick cake.


  6. #
    Juliaposted November 2, 2015 at 2:38 pm

    I absolutely adore this website. Both the pumpkin bread and the pumpkin snickerdoodles I made off of here are some of my favourite pumpkin recipes. Whilst I don’t at all agree with the folks that said this recipe is bland, I do feel there is a little something missing (more pumpkin spice? cinnamon? sugar?)  I would also personally double the cream cheese filling for next time. Overall, solid recipe. Thank you again for a winner :). 


  7. #
    Angieposted November 21, 2015 at 3:32 pm

    Can I use sweet potato? It’s very difficult to find pumpkin where I live.


  8. #
    Yolanda Liposted December 13, 2015 at 1:57 pm

    I made these last night, and when I went downstairs this morning, almost all of of them were gone! So I’ll definitely have to double the recipe next time, since there are so many people in our house (ten, to be exact). Thanks for an amazing recipe!


  9. #
    Erinposted December 15, 2015 at 2:38 pm

    Made these this morning for a snow day at home with a cup of highlander grogg. So delicious!


  10. #
    Andreaposted January 18, 2016 at 8:08 pm

    Amazing!!! Every recipe I make of yours is absolutely perfect! Scones, cookies, muffins, lemon layer cake!! Everything!! Thank you so much for sharing your recipes. I’ve tried other people’s and they always disappoint. These muffins were gone before they could cool! 


  11. #
    cookinggramposted May 18, 2016 at 11:07 am

    I did a test muffin and used store bought cheesecake in a tub . at finale, it seemed to be a little more fluid like than the pic. maybe the recipe is a little more consistent than the store mix.


  12. #
    Robinposted June 29, 2016 at 10:39 am

    These are in the oven right now! My house smells heavenly. I was going to add pumpkin seeds but forgot, but since I expect to make another batch soon I’d like to know if you have a suggestion for an amount? I was thinking half a cup and maybe adding half a cup to th crumble. The crumble didn’t work for me even after almost doubling th flour so I added 1/4 cup oats and got a crumble like mixture that is still yummy. I’ll add only the oats extra next time as it might be too flour-y with the extra flour. 


  13. #
    Jacqueline Rubalposted July 26, 2016 at 9:30 pm

    Phenomenal!!! Used gluten free flour so my celiac daughter could eat them…really outstanding… Almost as good as the lemon cupcakes with raspberry frosting…your recipes are so so good!!!


  14. #
    Shelbyposted July 29, 2016 at 12:53 pm

    These are the BEST muffins I have ever made!! They were absolutely delicious and soft and were a HUGE hit at my Women At Risk Jewelry Party in the Fall! I can’t wait to make them again this Fall! Thank you Thank you Thank you for this recipe!!! =D


  15. #
    Michelle Spauldingposted August 2, 2016 at 7:15 pm

    Do these have to be refrigerated since they have cream cheese filling, I want to send them to my daughter in California, and it will take 2 days via mail. Thanks


    • Sallyreplied on August 3rd, 2016 at 11:47 am

      They’re OK at room temperature for a couple days.


  16. #
    christinaposted August 7, 2016 at 12:44 pm

    Can i use frozen pumpkin puree? my mother in law made this from a fresh pumkin and froze it.


    • Sallyreplied on August 8th, 2016 at 7:52 pm

      Sure can– let it thaw first.


  17. #
    Tiffany Leposted September 4, 2016 at 3:56 pm

    I love how you combined all the flavors into 1 muffin!!(:
    I have a question, will the batter + crumb topping freezer well for a couple days in the freezer and would still be okay to bake? Will I have to thaw out the batter for a certain amount of time prior to baking? Thank you so much!!


  18. #
    Hollyposted September 15, 2016 at 8:52 am

    I melted the butter for the crumb topping and it came out too wet. I see your comment about leaving the butter softened in the topping now 🙁 however my cream cheese filling came out like water. I followed your instructions exactly, not sure what happened. The muffins taste like the do not have any cream cheese filling.


  19. #
    Danieposted September 21, 2016 at 11:06 am

    Could I substitute while wheat flour for the AP flour straight up? Or would other things have to be changed in the recipe to do that? If so, what changes would I need to make? 


    • Sallyreplied on September 21st, 2016 at 11:23 am

      Yep! No changes necessary– just an easy swap of flours.


  20. #
    Alyposted September 22, 2016 at 9:59 pm

    Can I sub neufchatel cheese for the cheesecake filling or will it all just ooze out?


    • Sallyreplied on September 25th, 2016 at 9:52 am

      Cream cheese is best.


  21. #
    Sheelaposted September 25, 2016 at 1:32 pm

    I made these today for to take to work, but instead of the streusel topping I drizzled the homemade salted caramel over top. Quite delicious!


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