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Like a delicious pumpkin roll, these pumpkin cream cheese 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 cream cheese-stuffed 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. First, I prepare a batch of homemade pumpkin pie spice. And then one of the first recipes I prepare each year are these pumpkin cheesecake muffins. I originally published this recipe in 2013 and it’s been a fall favorite since!

Everything to Love About Pumpkin Cheesecake Muffins

plate of pumpkin cheesecake muffins

3 Parts to Pumpkin Cream Cheese 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 they’ll be similar to my regular pumpkin muffins. You could also try these pumpkin crumb cake muffins or mini cinnamon sugar pumpkin muffins instead.
  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. It’s nearly the same crumb topping we use for peach muffins in the summertime.

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

Overview: How to Make Pumpkin Cream Cheese 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.

pumpkin muffin filled with cream cheese and topped with crumb

More Pumpkin Baking Recipes

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stack of pumpkin cheesecake muffins

Pumpkin Cream Cheese Muffins

  • Author: Sally
  • Prep Time: 25 minutes
  • Cook Time: 22 minutes
  • Total Time: 50 minutes
  • Yield: 1214 muffins 1x
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American

Description

Like a delicious pumpkin roll, these pumpkin cream cheese 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.


Ingredients

Scale

Crumb Topping

  • 1/3 cup (67g) packed light or dark brown sugar
  • 1 teaspoon ground cinnamon
  • 1/4 cup (60g) unsalted butter, melted
  • 2/3 cup (84g) all-purpose flour

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
  • 2 teaspoons ground cinnamon
  • 1 teaspoon store-bought or homemade pumpkin pie spice*
  • 1/2 cup (100g) packed light or dark brown sugar
  • 1/2 cup (100g) granulated 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

Cream Cheese Filling

  • 6 ounces (168g) block-style cream cheese, softened to room temperature
  • 1 egg yolk, at room temperature
  • 1/2 teaspoon pure vanilla extract
  • 3 Tablespoons (36g) granulated sugar

Instructions

  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: Mix the brown sugar, cinnamon, and melted butter together in a small bowl until combined. Add the flour and use a fork to gently mix 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, granulated 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.

Notes

  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: You can find pumpkin pie spice in the baking aisle of most grocery stores or make your own homemade pumpkin pie spice. If you don’t have either and want to use individual spices, use 1/4 teaspoon each: ground ginger, ground nutmeg, ground cloves, and ground allspice. This is in addition to the 2 teaspoons of cinnamon—you will still add that.
  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

Reader Questions and Reviews

  1. OMG! (My eyes almost popped out). Just baked this and YES.. thats after I took a bite from this muffin! I can definitely say this is the best recipe ever! It’s fluffy, it’s amazing in flavour, it’s not overly sweet, it’s it’s it’s… INCREDIBLE! I’ve followed the recipe closely (not even trying to be naughty by finding a substitute). The oven temperature really does the trick! My muffins were HIGH and they didn’t deflate. So if you haven’t try this recipe n thinking to make one, please make it! I got the same 14 portions. This muffin really made me want to sing. I’m in heaven…

    1. I haven’t made them yet but looking forward to do it. Question can I made this one day ahead? Or are they better on the same day?

      1. Hi Laura! It’s best to make and bake the batter right away, but the muffins can be stored at room temperature for up to 2 days or in the refrigerator for up to 1 week.

  2. These are delicious! Moist ,delicate, great flavor.
    I found they was a little too much extra strudel so next time I’ll half the recipe .
    Definitely a keeper

    1. These are requested by everyone that eats them! I use a piping bag to squeeze the filling into the middle. Can this recipe be made in a loaf and/or bundt pan?

      1. Hi Erica, We recommend a 9×5 inch loaf pan. The bake time will be longer. Use a toothpick to test for doneness

  3. My brother and I just made these and WOW! They are absolutely perfect. We followed the recipe exactly as written and these are definitely the best pumpkin muffins I’ve ever made. The remind me of the Starbucks pumpkin cream cheese muffins except they are so much better. Will be sharing with friends and family and adding to my muffin recipe rotation!

      1. Hi Miranda, that should be fine. Enjoy!

  4. Absolutely amazing. I just made them. So easy, so beautiful and super delicious. Will make again and will add to my favorite recipes. Thanks a lot.

    1. These muffins turned out awful!! They were intended for a church bak sale but ended up in the trash! They look beautiful on the outside but inside they were a gummy mess. BTW – I followed the recipes instructions as written, made NO substitutions and removed them from the oven when a toothpick came out clean! The cream cheese filling was overcooked and separated. The inside had the texture of wet clay. I’d like to post a picture of just how bad they are. I’ve been cooking for over 50 years but this has to be my worst faill!

      1. Hi Barbara, so sorry to hear that these muffins didn’t turn out for you! If the insides were gummy and the cream cheese separated, I wonder if you used full-fat block cream cheese? The kind sold in a tub has added water and is not suitable for baking, same goes for lower fat cream cheese. Thank you for giving these a try!

      2. Thanks for getting back to me. I did use full fat cream cheese and I figured out what I did wrong. I used the wrong amount and the filling just blew up
        That doesn’t explain why the cake part was so gummy.
        On a positive note, I used the leftover pumpkin puree to make your recipe for pumpkin cupcakes with cream cheese frosting. That was a 5 star+ recipe texture, frosting all delicious! Tender and moist – a winner!

  5. Best muffins ever! Followed the recipe and they came out perfectly. I prefer not to use cupcake papers when making muffins, and an ample spray of Bakers’s Joy in each of the 12 muffin tins worked great. Sally, your recipes never disappoint!!!

    1. Hi Annie, For mini muffins, bake at 350 degrees (the entire time) for about 12-14 minutes, give or take. Keep a close eye on them and use a toothpick to test for doneness.

  6. Second time making this recipe & both times got rave reviews. It’s in my recipe file

  7. I’m going to make these with fresh pumpkin puree instead of canned. Would it be a 1:1 substitution? I did let it sit for several hours in a nut milk bag to strain out extra liquid, if that matters.

    1. Hi Claire! We usually recommend blotting homemade puree since it is more wet, but you should be good to go if you’ve strained it. Happy baking!

  8. So excited to try these over the holidays! Out of curiosity… how do you think they would turn out in a bundt pan instead of as muffins?

  9. THE BEST MUFFIN RECIPE EVER!! I added freshly grated ginger root to the cream cheese recipe for an extra kick and more flavor. These muffins melt in your mouth and everyone is raving about how amazing they are! Thank you!!

  10. Hi, I made these before and they are delicious! I have some gluten-free friends though and wanted to make some for them. Can I substitute the flour for gluten-free flour?

    1. Hi Shelbie, we haven’t tested these muffins with gluten free flour, so we’re unsure of the results. Although some readers report using an all-purpose 1:1 gluten-free flour in many of our recipes with success, you should expect slightly different results anytime you substitute ingredients. Let us know if you give it a try!

  11. Just made these with my daughter and they turned out fabulous!! I substituted the vegetable oil with coconut oil due to dietary restrictions, and it worked just fine. This recipe is a keeper!

  12. I just made them for Thanksgiving. We are so full we haven’t had them yet. But they are beautiful! Instructions were easy to follow and easy to make. .

  13. OMG! These were awesome. Turned out perfect and they were gobbeled up so quickly. I will have to make morem

  14. I made these with tiny modifications to adapt to my pantry : i used an eat-me-today-or-Ill-die overoveroreverripe banana and completed with homemade pumkin purée (i had a shiatsu squash which has a fantastic chesnut and sweet taste). So i decreased the sugar by a third. I’m french and my flour is a little different (T65) so i had to add a little more (about 1/3 cup). I also inceeased baking time to a good 25 mn. It turned absolutely fantastic and i’m hooked. I had to put them in the freezer right after cooling so I didn’t eat them all ! This recipe goes into my hall of fame ! Thank you so much !

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