Pumpkin Cheesecake Muffins

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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

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.

Recipe 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.

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© 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. Some of the links above are affiliate links, which pay me a small commission for my referral at no extra cost to you! Thank you for supporting Sally’s Baking Addiction.

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!


  1. Cupcakes were pretty good.  I felt like there wasn’t enough cheesecake filling though. The cupcakes were slightly slightly dry so I think instead of 16min I will for sure do 15 min.

    I’m excited to try again though and tweet the recipie a little.

  2. 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! 🙂

  3. 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!

  4. 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

  5. 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

  6. 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. 

  7. 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!!

  8. 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 !

  9. 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!

  10. 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?

  11. 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

  12. 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!

  13. 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 😉

  14. 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! 🙂

  15. 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.

  16. 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!!

  17. 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