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. Cate @ Chez CateyLou says:

    Can I please have one of these for breakfast right now?? They look so good!! I can’t get enough pumpkin right now. I love your fall towels also, so cute and festive!

    1. Thanks Cate! I got them from Bed Bath & Beyond.

  2. Pumpkin cheesecake is definitely my favorite fall treat— it sounds absolutely divine in a muffin!– I love how the cheesecake filling peeks out from under the topping… Drool worthy. Pinned it!

    1. Thanks for pinning, Sarah.

  3. Katrina @ Warm Vanilla Sugar says:

    These are fabulous Sally! Love this recipe!

  4. Mallory @ Because I Like Chocolate says:

    Cheesecake and streusel, two of my favorite muffin additions!

  5. Kelli @ The Corner Kitchen says:

    Pumpkin, cheesecake AND streusel….sign me up!! Amazing muffins, Sally and so perfect fall chilly fall mornings!

  6. I’m loving that crumb topping on the top of these!

  7. These muffins look amazing! Now I know what to do with that can of pumpkin puree sitting in my cabinet. Thanks!

  8. Julie @ Table for Two says:

    I love all three parts of this muffin! I’m bias towards any crumb/streusel but man, you’re making it hard to choose with the addition of cheesecake! This is the perfect Fall muffin. I totally remember that day in October when it was 90 degrees. omg, threw me for a loop!

    1. Thanks Julie! And I think the 90 degree day was only like 2-3 weeks ago. It is 36 degrees in the suburbs of baltimore this morning!! Seriously…!?!

  9. Charmaine @ All in a Soiree says:

    Just stumbled upon your blog today loving your recipes.

  10. Jennie @themessybakerblog says:

    Oh lawdy, do these look good. I’m always excited for boot weather and fuzzy socks. I love this time of year. Pinned.

  11. I shouldn’t be allowed to view your page till at least 11am. Now I want sweets. These muffins look yummy! Strudel on top, yes please!!

  12. Ruthy @ Omeletta says:

    Gah, Sally, these look incredible. So much goodness stuffed into one little muffin! I’ll be clearing out my dishwasher in preparation of all the little bowls 🙂

    1. Haha! Yes, this recipe does have a lot of bowls going on. But after tasting one of these, you won’t even mind filling your dishwasher! Enjoy, Ruthy.

  13. Katie @ Veggie and the Beast says:

    I love the layers of flavor in these muffins! A good streusel gets me every time, and I want some of that cheesecake filling!

    We enjoyed FALL in MN for about a week, but then I had to break out my winter hat for the first time last night. I’m about ready to move from pumpkin beer to hot chocolate and Bailey’s 🙂

    1. Cold weather is completely worth it if you’re sipping hot cocoa with baileys. YUM.

  14. Beth @ bethcakes says:

    These look wonderful! Wish I’d had one (or two or three) with my coffee this morning. Especially because it finally feels like fall in the South too! 🙂 Love that cream cheese swirl and those chunks of streusel! Definitely worth some extra dishes to wash!

  15. Laura @ Lauras Baking Talent says:

    These look amazingly good! Please send a couple over my way… 🙂

  16. Valerie | From Valerie's Kitchen says:

    These look so comforting and have Fall written all over them! I’m so ready for Fall weather but here in Northern CA it’s still quite warm. Not quite boot weather yet!

    1. Once it cools off, you have to try these muffins Valerie! Or don’t wait. These still taste good in 80 degree weather. 😉

  17. Sally,
    everything you make either looks awesome(cause I haven’t tried it yet) or is awesome. You are an amazing baker!

    1. What a sweet comment. Makes my day. Thank you very much Carmen!

  18. Mimi @ Culinary Couture says:

    Best Fall muffin EVER! It’s been so cold in Jersey latey, I definitely need to snuggle up to one of these bad boys, and some hot chocolate with pumpkin spice marshmallows in the other hand 🙂

  19. Joy @ Baking-Joy says:

    Love these Sally, my husband is begging me to make pumpkin baked treats at the moment…am going to have to go hunting for pumpkin puree on the internet 🙂

  20. Nora (Buttercream Fanatic) says:

    This is one perfect fall breakfast! Or lunch….Or dinner…

    1. Or snack or midnight snack… 😉

  21. Anna (Hidden Ponies) says:

    I have lists EVERYWHERE, I love them! And the honey crisp apples…yum. Oh yeah, and these muffins? Awesome!

    1. I’m glad I’m not the only obsessive list maker.

  22. Laura (Tutti Dolci) says:

    With a cheesecake swirl and crumb topping, these are dream muffins!

  23. Oh my gosh!! These look absolutely amazing! I am going to make these tomorrow! Thank you for your hard work so that my weekend can be a little sweeter 🙂

  24. Oh my word these look AMAZING!! Must make a batch of these soon…

    Also, I got way too excited when you mentioned Centennial Park… I went to Centennial High School! Didn’t know anyone else knew about little ole Ellicott City. Even though I live in Bmore now, still love going home and running there!

    1. I used to live in Baltimore city, Barathi! For 4 years. And just moved to the county with my fiance. Loving it here! What a small world.

  25. Bouillon de Notes says:

    Thank you for this delicious combination, the pics are gorgeous, and look so tasty, cannot wait to bake some:)

  26. Ari @ Ari's Menu says:

    Seriously?? I mean, seriously. I can’t even handle these. Too many of my favorite things. Recipe love overload!

  27. Lucy @ Bake Play Smile says:

    Oh yum! Is there anything better than a cheesecake muffin! xx

  28. Dorothy @ Crazy for Crust says:

    These are fantastic Sally! And I need to do some October things before October is over!

  29. Liz @Life Made Sweet says:

    yay more pumpkin!!!! I can’t get enough and I totally agree pumpkin muffin pumpkin cupcake…I don’t care what you call it as long as it’s stuffed with cream cheese and topped with streusel it’s pumpkin delicious to me! 🙂

  30. Pamela @ Brooklyn Farm Girl says:

    This cheesecake looks great, but in muffin form – even better! I’ve been craving cheesecake, thanks for curing it! 🙂

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