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.

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.

cheesecake batter and pumpkin batter

pumpkin cheesecake muffin batter in muffin pan

crumb cake topping for 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

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

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 (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 (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

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


  1. Yum I just made these and they are soooo good! I think I am going to be eating them for breakfast and dessert…

  2. I made these muffins today and they were amazing! I’m in the process of learning how to bake and this recipe was super easy to follow. Thank you!

    1. I’m glad you tried these! They really are easy to make if you follow the instructions. I’m happy you love them! Thanks so much for taking the time to report back, Rokssana.

  3. I made these muffins yesterday and they’re so good! Sometimes I feel that a dozen muffins aren’t enough. With the extra two, it’s actually the perfect amount. Thank you so much for sharing this recipe! I think I’ll have to try again when it gets closer to Thanksgiving =)

    1. Thanks Andrea! I’m so happy you love these muffins. I’m making them again this weekend. They’re the best this time of year.

  4. Oh wow, I love pumpkin muffins already but these beauties with the cheesecake and streusel!! Save me from myself 😉

  5. OMG! These muffins are amazing! The family loved them! Great side to breakfast before church this morning!

  6. Thank you for a great recipe. These muffins are fun to make, they look good, they taste great, they smell amazing, and everybody loved them. I made them with homemade puree following a recipe similar to the one you posted, and it came out perfect.

  7. roselinflanders says:

    Just made these and they were a big hit I couldn’t wait for it to cool down. It’s a must make again!!

    1. Woohoo! Always happy to hear about this muffin recipe being loved by others. I love them so much.

  8. These muffins look amazing as all treats on your blog do. I’m not a huge fan of pumpkin so I was wondering what you though of substituting sweet potato? If so how would you alter this recipe.

    1. Hi Cathie. Cooked sweet potato is a fine replacement for the pumpkin in these muffins (use 1 cup mashed). In fact, I’d love to try that myself next!

  9. WOW, these look so yummy! I always make some kind of bread Thanksgiving morning, but I think this year I am going to mix things up and make these Pumpkin Cheesecake Muffins. Thanks for sharing 🙂

    1. What a great (and easy!) way to mix things up Thanksgiving morning Jenn! Hope everyone enjoys.

  10. Absolutely amazing! I just had one straight from the oven, super delicious, I did not know I was able to make such yummy muffins.
    Thank you for the receipe! The tip to use higher temperature to start with was great.

    1. Margaret, that’s fantastic. I’m happy you enjoyed these!

  11. second attempt at these rocked everyone’s world. (first batch had the problem of no phillie’s cream cheese in the country i live in. had to experiment with various cream cheese combos … and i forgot to put in the milk. whoops)
    I got sassy and made a graham cracker crumb base – kind of… no graham crackers so i improvised.
    great recipe. it will now be one of my standards.

  12. I just made these to take to a “Friendsgiving” tonight – they are absolutely amazing! Perfect combination of flavors. And they smelled so good while they were baking! So glad I stumbled upon these 🙂

  13. Let me just say,Starbucks aint got nothing on these muffins. I axtually went all oit and made everything from scratch. We had pumpkins left over from Halloween so I baked and pureed them. I also added a touch of lemon extract and cinnamon to the cream cheese filling. Great recipe the kids love them. Thanks keep’em coming.

  14. Hi Sally!

    I absolutely love your blog, I check it every morning when I wake up!! You have the best recipes. Everything I’ve made had turned out perfectly!! I am going to make these today for my moms birthday. I only can find my mini muffin pan so I’m going to try it in those. I’ll let you know how it goes 🙂

    1. Hi Kelly! Happy Birthday to your mom. And thank you for the sweet comment! I’m happy you enjoy my blog. Filling mini muffins with the cheesecake may be tough and you might have a lot of cheesecake batter leftover since the mini muffins can’t hold nearly as much as 14 muffins can. Regardless, I hope you both enjoy!

      1. They turned out perfectly!!! They are so cute too 🙂 I used about a teaspoon of batter on the bottom, teaspoon of cream cheese mixture and then filled the rest with batter. Then topped with streusel. It made 48 mini muffins perfectly 🙂

        Thank you Sally, your recipes are truly amazing and thank you for spending the time to test recipes and provide such thorough instructions 🙂

      2. Kelly, that’s great! Thank you so much for taking the time to write back.

  15. Hey Sally!

    I want to make only the muffin portion of this recipe. (I know, I know! It’s not what you originally created) How much dark brown sugar should I add if I’m just making the muffin part? Since I know the sweetness of the muffins will be different just by themselves.

    Thanks in advance! 🙂

    1. Hi Hima , the muffin part is actually this exact recipe, minus the chocolate chips and frosting: https://sallysbakingaddiction.com/2013/08/18/pumpkin-cupcakes-with-dark-chocolate-frosting/

      So you only need 1/2 cup of dark brown (or light brown) sugar for them.

  16. just made these and as usual, they turned out amazing! your recipes never disappoint! I’m sure these won’t last long in my house!

  17. Eating one hot out of the oven right now! DELICIOUS! They baked up beautifully and look every bit as good as they taste!

  18. First time visitor to your blog and will visit regularly now! I wanted to make a pumpkin cheese cake for Thanksgiving, but stumbled upon this recipe. I made these for our Thanksgiving breakfast today and my hubbie had three in less than 3 minutes…LOVED them! I really liked them, but other streusel I’ve had have been sweeter and crispier. I could taste a bit too much the flour…do you think I could reduce the amount of flour and increase the brown sugar? I can’t wait to make them again just need help on the streusel 🙂 Happy Thanksgiving!

    1. Hi Liz! So happy that you both enjoyed the muffins. And yes, you may certainly tweak the streusel however you see fit! It’s not super sweet, I agree. Perhaps do 1/3 cup of each, so you are reducing the flour and increasing the sugar. Happy Thanksgiving!

  19. Wow! What a great recipe! A friend gave me a huge pumpkin from their garden so I have been looking for great recipes to use up the pumpkin purée that I made. The muffins have a great texture and are not too sweet. I had to use two tablespoons of batter, then two spoonfuls of cream cheese mixture, then another two tablespoons of batter for the size to work out, but the baking time and temperature was exactly right.
    This is the first time I have come across your site. I will definitely browse more of your recipes for ones to try. Thank you!

    1. Very glad you loved these, Megan! Thanks for reporting back. Let me know what you make next!

  20. I made these for Thanksgiving. Yummy and so much fun to make! I’ll definitely be making these again. Thanks!

  21. I’m using your recipes to make delicious gluten-free baked goodies by substituting Cup4Cup flour.

  22. So glad you enjoyed these pumpkin muffins, Trixie! Yours sound wonderful. For your questions: 1) no need to adjust the BP or BS 2) You may certainly add flax, but I would not take out more than 1/4 cup of flour in this recipe without heavily affecting the baked muffin’s texture.

    1. Thanks, Sally, for the speedy reply. It’s wonderful to be able to ask a professional baker these random questions. Enjoy the rest of your Sunday!

  23. I adored this recipe! I underbaked mine just a little bit so that the cream cheese would still be creamy and not stiff. I really loved these muffins. They were delicious. I posted about them in my blog post today if you’d like to take a gander at it. (:
    Thank you for this!

  24. Just wanted to say thanks for this recipe. They are easily the best muffins we’ve ever had. Thank you also for the gram measurements – I wish more recipes were listed this way. Fabulous, well written recipe.

  25. Does it matter if you use reduced fat cream cheese in the cheesecake filling? I want to make these but all I’ve got in the fridge is the reduced fat kind and I’m kind of too tired to go to the store.

    1. I don’t like the texture (less creamy) with low fat creamy cheese, but it would definitely work here if you have no other option.

      1. Thanks for replying! Just wanted to let you know I DID use the low fat cream cheese and I didn’t taste the difference so all was well!

  26. I just tried making these. Of course I started mixing ingredients before realizing that I actually didn’t have any pumpkin puree! I just swapped in 1 cup of some mashed sweet potatoes, as another commenter mentioned.

    The spice cake part was perfectly spiced. The cheesecake part was creamy and delicious. The streusel was a tad too floury on its own, but tasted just fine when eaten all together. I ended up with exactly 12 muffins, even though I measured everything on a kitchen scale. *shrug* no big deal.

    The only issue I had was that they came out of the oven beautifully domed, but after cooling, it collapsed in the middle (like a sad soufflé). Any idea what could have gone wrong? I followed everything to a T.

    Thanks again for the wonderful recipes and pictures!

  27. I can’t wait to try these muffins!!! I’ll definitely be back 🙂

  28. Can’t wait to try them!

    I am watching my calorie intake so I’m wondering how to “lighten” up the recipe. What substitutions would you make? Thanks!

    1. Hi Aimee – I’m unsure without testing myself. But here are all of my healthier recipe options if you care to browse: https://sallysbakingaddiction.com/category/healthy-recipes/

  29. We are home schooling our 6 year old daughter. She loves to watch the baking shows. Part of her curriculum is cooking (with daddy). We are going to make these muffins. They look delicious!!

  30. Hi Sally,
    Would it be ok to sub half the oil for applesauce like in your zucchini bread recipe? Also, can I sub butternut squash for the pumpkin?

    1. hi Robin – I’ve never tried subbing applesauce in these muffins. But it’s worth a try. I fear they would taste rubbery. And butternut squash is a great sub for the pumpkin.

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