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!


Comments are closed.

  1. Sally, the muffins were delicious, (we ate almost a whole batch in one day!!) but when I try to print the recipe, it says “no posts match your criteria”. Is it just my computer?

    1. Thanks Taylor – I’m currently working to have this temporary bug fixed!

  2. I made these for a camping trip I went on last weekend and they were a huge hit! I made 6 jumbo muffins instead of the 14 smaller ones and it was the perfect amount of batter! Great recipe!

  3. I made these this morning and my daughter, who dreads my fall pumpkin obsession LOVED these. I added chopped pecans to the topping mixture and they turned out beautifully!!! Only made 1 batch, next time I’ll double it since I was asked to make more tomorrow.

  4. Just came across your website last night – holy cow do I have a lot of recipes on my ‘to try’ list now! I made these and the sky high apple pie muffins today and both have rave reviews from my mother (who I made them for, and who is also quite picky when it comes to baked goods!). She loves that they’re not too sweet. As soon as she tried a pumpkin cheesecake muffin she promptly put most of them in a ziploc freezer bag and hid them from her husband in the freezer so that they won’t disappear too fast!

    1. Sounds great Catherine. Thank you so much for reporting back on both muffin recipes. Let me know any other recipes you try!

  5. Thanks for linking to these through your recent cheesecake post. Although I’m generally anti-muffin as I consider them “not quite cake so why bother”, these ones look like something I could make an exception for in my daily diet. 😉

    1. not quite cake so why bother — hahahahaha I’m laughing so loud. You’re absolutely right. But it sort of makes you feel like you’re eating cake for breakfast? You have to try these!

  6. These were delicious! A big hit all around and I will be making them again soon.

    I ended up with leftover streusel topping, but no biggie. Next time, I’ll make a little extra of the cheesecake part and go heavier on that (I didn’t think they had quite enough).

  7. Mmmmm. Totally LOVE these muffins 🙂

  8. I never know when I have to refrigerate something that has cream cheese in it? Do these need to be? Thanks.

    1. These are actually just fine at room temperature (tightly covered) for 3 days. Any longer than that, stick in the refrigerator.

  9. the recipe for the muffin itself is not listed..

  10. I just made these and tried one and they really are amazing! My husband and daughter loved them too. These will definitely be something I make again and again. Thanks so much for the delicious recipe!!

  11. I’m so excited to make these I’m just learning how to bake…I’m going to use pumpkin cream cheese instead to make it even more pumpkiny 🙂 thanks for the great recipe they look so yummy!

  12. These turned out lovely! Great combination of flavors and textures. Thank you for sharing your recipe!

  13. These are amazing! I am just wondering if there is a recipe to double this? I want to make these for thanksgiving but fear that 12 will not be enough because of how delicious they are!

    1. Simply double all the ingredients – and thanks for reporting back!

  14. I made these as 24 mini muffins + 6 standard muffins. Since I used both the cheesecake filling and streusel topping too sparingly on the mini muffins, I had both leftover when the pumpkin batter ran out. I put the rest of the filling in a bake-able mise en place bowl, sprinkled on some of the topping, and baked it along with the muffins. That on its own was amazing and will have to be repeated as a simple quick cheesecake! I must also rave about the perfectly domed tops on the muffins. I hate when muffins spill over and deflate.

  15. I have a leftover pumpkin cream cheese cheesecake dip but I’m not sure what I can do with. And has the ingredients of your cheesecake filling minus the egg yolk, and a handful of extra ingredients like pumpkin pie mix and some spices and seasoning. I’m wondering if I can use it in place of your cheesecake filling. I’m not the best baker so my biggest concern will be the chemistry behind it. I need the egg in order for it to set up or with out it will it goop everywhere, or if I can add an egg to what I’ve already got and get the same science.

  16. I was so excited to try these. They took forever but the reviews were good. When I bit into one I was sorry I spent all night making them. They had no flavor and I added extra pumpkin spice. I went over the measurements with my husband and did everything exact. We bake all the time and these were just so bland. They are not worth all the labor you have to put into them. Worst idea in a long time. I don’t understand all the amazing reviews I did everything and didn’t overcook them; they still were the most tasteless muffins I’ve ever had (including gas station ones).

    1. I thought the same thing. I spent all morning making them, but my husband and I both agreed that they didn’t have much flavor. I checked and double checked the recipe, but I didn’t miss anything. Not sure what happened.

  17. Hi! I was wondering if the baking time/temp would change if I don’t add the cream cheese filling. just realized that I forgot to buy the cream cheese when I was buying ingredients! thanks!

    1. Time may be slightly reduced; but the temperature is the same.

  18. Thank goodness for Pinterest. Found this recipe and tried it out after a long and gray snowy day yesterday. I let them completely cool and then put them in tupperware for my co-workers the next day. I actually thought they were better on day two. Warm up for 10 seconds and YUM! Thanks for the work you did to piece this recipe together.

  19. Wow! I cooked down fresh pumpkin today,looked for a recipe found this and the rest is history. They are yummy. already made a second batch. Mine are the size of costco muffins.Thankyou for this recipe. excellent flavor,texture I’m addicted Thanks

  20. Hi Sally,
    I chanced upon ths recipe & your webite yesterday while seaching for pumpkin cheese bakng recipe. My pumpkin cheesecake recipe turned out great! I love them and I must say your recipe is so fun and creative. I am going to try out the spinach quiche next. Thanks for sharing!!!

  21. I wish I could post the pictures I took of these beauties! I made these for my boyfriends cousin and his fiancee and they were blown away by these muffins. I won’t use another recipe for pumpkin muffins. I can’t. Not after seeing how sexy these babies came out of the oven. I could box these things up and no one would know I didn’t buy them at a bakery.

    Thank you!

  22. 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!

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

  24. 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!

  25. 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!    

  26. Theses sound amazing~ But…
    Not wanting to sound stupid but is canned pumpkin the same as puree? If not what do I buy instead ?

  27. Can I substitute Applesause for oil in the pumpking creamcheese muffins/

  28. 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!

  29. Hello, I made these muffins recently, and although they turned out incredibly delicious, my cream cheese filling inside was gone! Did I over cook them! I did leave them in the pan for longer than 10 minutes, could that be the problem?

  30. 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).  

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