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

  2. 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? 

    1. 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.

      1. 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? 

    2. 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! 

    3. Rachel Schiffer says:

      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.

  3. 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! 

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

    1. 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.

  5. 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 :). 

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

  7. 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!

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

  9. 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! 

  10. cookinggram says:

    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.

  11. 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. 

  12. Jacqueline Rubal says:

    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!!!

    1. I was wondering about gluten free flour. What did you use and how did they turn out?

      I’ve made been searching for a GF pumpkin cheesecake muffin/cupcake recipe and this seems spot on! 

  13. 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

  14. Michelle Spaulding says:

    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

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

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

    1. Sure can– let it thaw first.

  16. 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!!

  17. 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.

  18. 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? 

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

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

    1. Cream cheese is best.

  20. 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!

  21. Would I be able to bake this as a loaf instead of the muffins?

    1. Absolutely. Just layer the batter, the cheesecake, more batter, and the streusel as the directions instruct for muffins. I’m unsure of the proper bake time.

  22. Christine S. says:

    I just made these but I did so with a large muffin pan. They only made 6 big muffins and while they’re very good, I’ll make a few changes next time. Since I made a large muffins I will make additional cream cheese filling to go in them. I will also add more spices. Although these were good they weren’t quite as rich and cinnamony flavored I had wanted. The topping didn’t crumble the way it said it would but I just laid it on top of them and push down and it turned out fine. They are good, they smell Heavenly, but just need a little bit more flavor for my taste. I could not find instructions for large muffins so I added about 10 minutes more time to them. I checked them with a knife to see that it came out clear of muffin do even though it had some cream cheese on it. I will definitely make them again. 

    Do you think I can somehow incorporate pumpkin puree instead of spice somehow? I don’t have pumpkin spice!

    1. I have a recipe to make your own pumpkin spice if you would like it

  24. Does anyone know how many muffins this recipe makes. .I might have to double it. Lol sounds so good.

  25. These muffins have been a favorite in our house ever since you posted them. Every fall since my daughters ask me to make them, and now I’m about to. Would the same recipe work if I make it as a cake or as bars? What size of pan? Thanks!

  26. I just made these. Came out ok. Could use a little more spices. I only got 9 muffins. Don’t know if I’ll make again, to much work for 9 muffins.

  27. These are delicious!! I doubled the recipe and got almost three dozen, (I guess they were not filled to the top of the muffin cup). Everyone in my family loved them!! Winner!!

  28. These look scrumptious and I’m making them today. Just wanted to say how very much I appreciate you doing the ingredients by weight! I find that when I stick to weights, I get consistent results every time! For inexperienced cooks, it takes the worry out of ‘is the batter too thick/thin’, etc.

  29. 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.

  30. 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! 🙂

    1. Elizabeth, So happy the muffins (cupcakes 🙂 ) worked well for you! Enjoy the donuts – what a fun baby shower treat!

    2. Kimberly Yanez says:

      I made these today, I’m not much of a baker, it’s just too precise for me , it’s a science. That being said, I had absolutely no problem with thr typing or any party if this recipe. Turned out beautiful, thank you so much. It was fun and I’ll make them again!

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