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. 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!

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

  3. 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!

  4. Murphy Miller says:

    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!    

  5. 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 🙂 )

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

  6. 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).  

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

  8. 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.

  9. 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! 

  10. 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!

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

  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!!!

  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. 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.

  17. 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!

  18. 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.

  19. 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!!

  20. 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.

  21. 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.

  22. 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! 🙂

  23. These are great and moist and the cream cheese filling cooks perfectly but overall they are not sweet enough

  24. 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.

  25. 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

  26. 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!

  27. Christina Oelze says:

    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. You can use either – I personally love cinnamon so for these muffins I wanted more of that flavor!

      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?

      2. I use 1 tsp pumpkin pie spice and 1.5 tsp cinnamon

  28. 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!

  29. Hi Sally, made these for my co-workers and the loved them. Thank you 🙂

  30. HI! Can I use cake flour instead?

    1. I recommend all-purpose flour.

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