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. Yes and yes!! Pumpkin and cheesecake belong together — love the sound of these muffins. I’ve seen a lot of cheesecake fillings with just the yolk and never knew why — thanks for the tip!

    1. Yes! Just the yolk will give the filling a cheesecake texture and taste. The egg white made it taste very, very egg-y. Not good!

  2. Averie @ Averie Cooks says:

    The crumb topping AND the filling. I could eat a big bowl-full of each and be super happy 🙂 I bet with all the textures going on, these were a dream to devour.

    The outdoor nature pic is so pretty. I look at palm trees so seeing leaves, that are brown or orange – reminds me of my childhood!

    1. I would gladly take your palm trees today, Averie. It is 36 DEGREES this morning!!

  3. I am all about that crumb topping! So darn good, Sally! These are just awesome! 🙂

    Fall is long gone here. It came late September/early October and was gone within a week. Snow hit and leaves fell. Pretty sad since I LOVE fall. Your pics of the water and trees is gorgeous!

    1. Kevin used to live in CO (that’s where you are, right?) and he tells me all the time how gorgeous fall is there, but how VERY short it is! 🙁 I will be sure to post more pictures of some views so you can enjoy it along with me!

  4. Yvonne @ bitter baker says:

    Oh wow, these look amazing! I won’t eat muffins unless their moist, so these are literally calling my name. Plus I love pumpkin and cheesecake!!

    1. Yvonne, I have the same feelings about muffins. I cannot stand muffins that are dry!

  5. this view is as gorgeous as those muffins look good !!!

  6. Centennial Lake? You must be a Howard County gal! I used to go there all the time when I lived in the area. Still a Ravens fan!

    1. I sure am! Go Ravens. =)

  7. Isis LittleMiracle says:

    These lovely muffins is so marvelous! Thank you for wonderful pictures and a good recipe! LOVE YOUR BLOG!

    1. Happy ou love my blog! And let me know if you give these muffins a try. Have a great day Isis!

  8. Midnight pumpkin snack for the win. I completely understand why there would be no self control around these… they look incredible! And where is that beautiful park/lake? In Baltimore? Gorgeous! Glad you’re enjoying October!

    1. Lake Centennial is in the suburbs of Baltimore. It’s a gorgeous spot for sure!

  9. Eat Good 4 Life says:

    These muffins look awesome. I have been making quite a few pumpkin recipes too 🙂 My husband is an super beer fan so I have been trying some pumpkin beers as well, however, I can’t taste the pumpkin on any of them 🙂 I don’t know maybe my taste buds and not quite on point!! By the way I saw on FB that you posted you were going weeding dress shopping. Congrats, I did not know 🙂

    1. I went wedding dress shopping yesterday. I think I found the one! Thanks so much 🙂

      And pumpkin brews – I find that they don’t strongly taste like pumpkin either, but it really depends on the brew. I like Blue Moon Pumpkin Ale on draft. Tastes the most pumpkin-y to me.

  10. Alexe @ Keys to the Cucina says:

    OMG, pumpkin + cheesecake? Two of my favorite things and you’ve kncocked this one out of the park!

  11. Do you think you could make this into a loaf or a coffee cake? I made and loved your pumpkin coffee cake and I feel like adding a cheesecakey layer to the mix would take it over the top 🙂 Also this could be a silly question.. is your muffin tin any larger or different than a cupcake tin?

    1. Hi Chelsea, no my muffin tin is a standard 12-count tin. I had to bake two batches since there are 14 muffins. You could certainly use this recipe to make a loaf (9×5 pan) or coffee cake (9×9 pan or 11×7 pan, no smaller). Just layer the batter, the cheesecake, more batter, and the streusel as the directions instruct for muffins. I am uncertain about the baking time for either though.

      1. Sally, I used your recipe with a 9×9 pan today, so I thought I’d tell you my timings; I have a fan oven, so I did the first 5 min at about 400F, then turned down to about 325F for the remaining time. All in all, the mix was baked fully (clean skewer with a few crumbs clinging) after approx 28 min. I’ve had a piece (okay, two!) and it turned out incredibly. I’ll definitely be trying many more of your recipes!

      2. Must try this as a pumpkin/cheesecake/streusel cake, Carolyn! Happy you love it. Thanks for reporting back! I appreciate it because now I have something new to bake with this batter. 😉

  12. Oh my gosh, cheesecake (and cream cheese generally) make everything AMAZING. I love the idea of stuffing a muffin with cheesecake…and heck, I’m not against frosting them as well. 😉 Cupcake, muffin, whatever. The pictures are great…you really caught the different layers and the streusel looks gorgeous! 😀

    1. Thanks Caley! I wasn’t 100% about the photos, so I’m happy you like them. These are practically cupcakes that are disguised as muffins. Love it.

  13. Jess @ On Sugar Mountain says:

    Woohoo for fall weather! And WOOHOO for these muffins! I want them ALL – seriously. I clicked my heels three times: that should mean a muffin, appears right? 😉

    1. Hahaha Jess you’re hysterical.

  14. Julie @ Lovely Little Kitchen says:

    These muffins are really calling my name! By the way, just finished reading through all your photography and blogging tips. I’m a newbie here, and I really appreciate the time you took to share what you’ve learned so far. Thanks!

    1. Hi Julie! Welcome to my blog. I’m happy you were able to read through my blogging tips and even happier you found some of them helpful. Have a great weekend!

  15. Rachel @ Baked by Rachel says:

    Love these muffins Sally! Great job.

  16. Stephanie @ Eat. Drink. Love. says:

    The muffin queen strikes again! I love seeing that cheesecake sticking out!

  17. I am decidedly NOT a muffin kind of gal–usually–but I love and love some more these already. I have been swirling cheesecake into every baked goods I can get my hands on, and these sound perfect. How does that song go? Hey, I just met you, and this is crazy….. 😉 thanks for sharing!

    1. Haha Ala that song is great- so catchy! And I think you’d really like these!

  18. Chung-Ah | Damn Delicious says:

    The view is just gorgeous, And these muffins with the secret cheesecake filling – pure genius! And I CAN have it for breakfast! Score!

  19. I can’t even.. no words. So many of my favorite things combined into one. This blog is making me go broke will all the baking I’m doing but it’s beyond worth it. So excited to make these next. It’s going to be great with some hot apple cider.

    1. I just had hot apple cider yesterday. And YES it would’ve been perfect with these muffins Kate!

      Baking is so worth the extra $$. It makes you and all the taste testers around you happy. Enjoy!

  20. Renee @ Two in the Kitchen says:

    Pumpkin muffins stuffed with CHEESECAKE?? Amazing! Oh, and I am more than ready to finally be wearing my boots.

  21. I just made a couple of these and can’t wait to try them! But was it right, that my batter was so liquidy? I hope, the layers stayed in the right order, they seemed to sink into one another.
    However, thank you for providing gram am ml measurements, that makes it so much easier for me!

  22. Abbie @ Needs Salt says:

    Oh my goodness you did everything with these muffins. Seriously – they are just perfect! I need one right now alongside a nice cup of tea. <3

  23. Grilling at the beach. That sounds like an awesome time! I already sorta miss the summertime. Have fun Renee!

  24. Each element of these muffins looks perfect Sally! I love anything with a crunchy streusel topping!

  25. Hayley @ The Domestic Rebel says:

    These look like Starbucks version but like, eleventy million times BETTER. Look at that cheesecake tucked inside! So heavenly, yet so sinful at the same time. And I checked my calender and yep, I am definitely available to be your muffin guinea pig. Send ’em on over!

    1. Hahahahahaha I am cracking up. You can always be my muffin guinea pig. I’m hiring!

  26. These look AMAZING! I’m so addicted to cheesecake right now, I definitely need to give these a go 🙂 Thank you for sharing the recipe.

  27. Trish - Mom On Timeout says:

    Love anything cheesecake and I am currently obsessed with pumpkin – MUST try these ASAP! Pinned 🙂

  28. they look delicious!

  29. Sally, these were an instant hit with friends and family. Just the right amount of sweetness in the pumpkin batter make these muffins a great breakfast (as well as anytime) snack. Thank you so much!!!

  30. I know exactly what you mean about averaging 3 pumpkin muffins a day. I cannot resist!

1 2 3 4 6

Leave a Reply

Your email address will not be published.

This site uses Akismet to reduce spam. Learn how your comment data is processed.

With kitchen-tested quality recipes and step-by-step tutorials, my goal is to give you the confidence to bake and cook from scratch.

Sally's signature

Recipes You’ll Love



Join the community on the 1st of every month as we tackle a new challenge recipe. Review Sally's Baking Challenge FAQ page if you have any questions.

View More

A tradition since 2013, every December we countdown to Christmas with 10 new cookie recipes in a row!

View More

The first week of every November is all about Thanksgiving Pies.

View More

My Cookbooks

Sally's Cookbooks

About Sally

Welcome to my Kitchen!

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