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!

178 Responses to “Pumpkin Cheesecake Muffins.”

  1. #
    Maryposted October 11, 2014 at 10:19 pm

    I just made these and tried one and they really are amazing! My husband and daughter loved them too. These will definitely be something I make again and again. Thanks so much for the delicious recipe!!


  2. #
    Brienneposted October 15, 2014 at 11:53 am

    I’m so excited to make these I’m just learning how to bake…I’m going to use pumpkin cream cheese instead to make it even more pumpkiny :) thanks for the great recipe they look so yummy!


  3. #
    Rachelposted October 24, 2014 at 1:05 am

    These turned out lovely! Great combination of flavors and textures. Thank you for sharing your recipe!


  4. #
    Lizzieposted October 26, 2014 at 5:32 pm

    These are amazing! I am just wondering if there is a recipe to double this? I want to make these for thanksgiving but fear that 12 will not be enough because of how delicious they are!


    • Sallyreplied on October 26th, 2014 at 5:46 pm

      Simply double all the ingredients – and thanks for reporting back!


  5. #
    Cyndiposted October 28, 2014 at 7:16 am

    I made these as 24 mini muffins + 6 standard muffins. Since I used both the cheesecake filling and streusel topping too sparingly on the mini muffins, I had both leftover when the pumpkin batter ran out. I put the rest of the filling in a bake-able mise en place bowl, sprinkled on some of the topping, and baked it along with the muffins. That on its own was amazing and will have to be repeated as a simple quick cheesecake! I must also rave about the perfectly domed tops on the muffins. I hate when muffins spill over and deflate.


  6. #
    Samantha Lposted November 3, 2014 at 8:50 am

    I have a leftover pumpkin cream cheese cheesecake dip but I’m not sure what I can do with. And has the ingredients of your cheesecake filling minus the egg yolk, and a handful of extra ingredients like pumpkin pie mix and some spices and seasoning. I’m wondering if I can use it in place of your cheesecake filling. I’m not the best baker so my biggest concern will be the chemistry behind it. I need the egg in order for it to set up or with out it will it goop everywhere, or if I can add an egg to what I’ve already got and get the same science.


  7. #
    Lexiposted November 11, 2014 at 7:17 am

    I was so excited to try these. They took forever but the reviews were good. When I bit into one I was sorry I spent all night making them. They had no flavor and I added extra pumpkin spice. I went over the measurements with my husband and did everything exact. We bake all the time and these were just so bland. They are not worth all the labor you have to put into them. Worst idea in a long time. I don’t understand all the amazing reviews I did everything and didn’t overcook them; they still were the most tasteless muffins I’ve ever had (including gas station ones).


    • Daniellereplied on September 13th, 2015 at 10:05 am

      I thought the same thing. I spent all morning making them, but my husband and I both agreed that they didn’t have much flavor. I checked and double checked the recipe, but I didn’t miss anything. Not sure what happened.


  8. #
    Lois Kimposted November 11, 2014 at 6:35 pm

    Hi! I was wondering if the baking time/temp would change if I don’t add the cream cheese filling. just realized that I forgot to buy the cream cheese when I was buying ingredients! thanks!


    • Sallyreplied on November 11th, 2014 at 6:36 pm

      Time may be slightly reduced; but the temperature is the same.


  9. #
    Jamieposted November 17, 2014 at 9:36 am

    Thank goodness for Pinterest. Found this recipe and tried it out after a long and gray snowy day yesterday. I let them completely cool and then put them in tupperware for my co-workers the next day. I actually thought they were better on day two. Warm up for 10 seconds and YUM! Thanks for the work you did to piece this recipe together.


  10. #
    vickyposted November 18, 2014 at 1:28 am

    Wow! I cooked down fresh pumpkin today,looked for a recipe found this and the rest is history. They are yummy. already made a second batch. Mine are the size of costco muffins.Thankyou for this recipe. excellent flavor,texture I’m addicted Thanks


  11. #
    Pin Sinposted November 30, 2014 at 3:53 pm

    Hi Sally,
    I chanced upon ths recipe & your webite yesterday while seaching for pumpkin cheese bakng recipe. My pumpkin cheesecake recipe turned out great! I love them and I must say your recipe is so fun and creative. I am going to try out the spinach quiche next. Thanks for sharing!!!


  12. #
    Jamesposted February 6, 2015 at 2:29 am

    I wish I could post the pictures I took of these beauties! I made these for my boyfriends cousin and his fiancee and they were blown away by these muffins. I won’t use another recipe for pumpkin muffins. I can’t. Not after seeing how sexy these babies came out of the oven. I could box these things up and no one would know I didn’t buy them at a bakery.

    Thank you!


  13. #
    SavvyChefposted April 6, 2015 at 12:22 pm

    I just made these and loved them! I ended up with 16 full muffins using a cupcake pan and tested out the first pan baking at 425 and reducing the temperature to 350 after 5 minutes and the other pan just baking it all at 350…there was a slight but EXTREMELY negligible difference in how much they rose. I think only someone who will lean down to the edge of the counter to measure the difference could tell lol. I swapped out 1/2 the oil for fat free sour cream and half the flour for oat flour that I ground at home. I also used almond milk instead of regular and increased the cinnamon. They were SUPER moist and delicious! For the crumb topping I did a mixture of melted butter, brown sugar, cinnamon, whole oats and chopped pecans. DELICIOUS muffin, can’t wait to bake it again during the fall!


  14. #
    Pamposted May 10, 2015 at 1:43 pm

    Made these today. WOW!!!! (to the tenth power) `nuff said.


  15. #
    Micheleposted August 10, 2015 at 12:12 pm

    These were amazing!! I used the full 8 oz. block of cream cheese because I know the extra 2 oz. would just go bad in my fridge before I used it. It made exactly 14. These are the best muffins I’ve ever made–and I’ve made a lot of pumpkin muffins! This is what I’ve been looking for! Thank you! These are so fluffy and light and perfectly spiced!


  16. #
    Murphy Millerposted August 12, 2015 at 10:07 pm

    This recipe has no faults, it was beyond delicious. They by no means lasted longer then a day in my house. Cheers for this one!    


  17. #
    Kathleenposted August 22, 2015 at 3:07 pm

    Theses sound amazing~ But…
    Not wanting to sound stupid but is canned pumpkin the same as puree? If not what do I buy instead ?


    • Sallyreplied on August 22nd, 2015 at 4:47 pm



  18. #
    Lindaposted September 22, 2015 at 5:47 pm

    Can I substitute Applesause for oil in the pumpking creamcheese muffins/


  19. #
    Mabelposted September 24, 2015 at 12:02 am

    These look fantastic! Seriously – pumpkin + cheesecake + crumb topping = absolute fall heaven. 

    The only thing that’s keeping me from jumping up and making these right now is this – can pumpkin puree be substituted for canned pumpkin? It’s all I have on hand. (This goes for pretty much all of your amazing pumpkin recipes as well, so a quick reply would be greatly appreciated :) )


    • Sallyreplied on September 24th, 2015 at 7:41 am

      fresh pumpkin puree can definitely be used in these muffins instead of canned. For most of my pumpkin recipes, too. Enjoy Mabel!


  20. #
    Allyssaposted September 27, 2015 at 9:36 pm

    Hello, I made these muffins recently, and although they turned out incredibly delicious, my cream cheese filling inside was gone! Did I over cook them! I did leave them in the pan for longer than 10 minutes, could that be the problem?


  21. #
    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).  


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