Pumpkin Cheesecake Muffins

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Super-moist pumpkin spice muffins stuffed with cheesecake filling and topped with brown sugar cinnamon streusel.

Pumpkin muffins filled with cream cheese filling and topped with sweet cinnamon brown sugar streusel!

It’s finally starting to look and feel like fall around here. We had a few really chilly days in September, and then a 90F degree day in October (seriously?!), and now we’re into fuzzy slipper and cute boot weather. Surely you get excited about fall just to break out your boots again, right?

I spent this past weekend crossing some things off my fall to-do list. I went out for pumpkin beers, bought a couple pumpkins to carve, stocked my fridge with locally grown Honey Crisp apples (and umm… they’re almost already gone), and we took Jude for a long walk at Centennial Park.

Seriously, look at this view:

Walk w Jude

To round out my super spirited October weekend, I made a couple test batches of pumpkin muffins. Stuffed with cheesecake and topped with streusel. Because what’s a muffin without some streusel?

They’re like a pumpkin roll turned into a muffin. Or an inside out cream cheese-frosted pumpkin bar. Cheesecake meets pumpkin pie meets crumb cake.

Pumpkin muffins filled with cream cheese filling and topped with sweet cinnamon brown sugar streusel!

There will be a lot of little bowls happening on your counter when you make today’s muffins. Sadly, that means more dishes to wash. But do extra dishes even matter when the end result is this?!

There are three parts to today’s recipe.

(1) Super-moist spiced pumpkin muffins.

(2) 4 ingredient cheesecake filling.

(3) Easy brown sugar streusel.

Let’s start with the muffins. The muffins themselves are lightly sweetened with brown sugar and left moist from pumpkin puree, oil, and eggs. You’ve actually seen them before on my website. I used this muffin batter to make cupcakes a couple months ago. With the addition of dark chocolate frosting and chocolate chips, my pumpkin muffin batter was seriously dessert-i-fied. You might want to check them out.

Pumpkin cupcakes vs pumpkin muffins. Where do you draw the line? I really don’t care where the line is between the two, especially if dark chocolate frosting or cheesecake filling are involved. Moving along…

Pumpkin muffins filled with cream cheese filling and topped with sweet cinnamon brown sugar streusel!

Next – the cheesecake filling. Oh baby. This stuff is good. You’ll only need four little ingredients: cream cheese, sugar, vanilla, and 1 egg yolk. I found that when I used an entire egg for this filling, it tasted eggy. Like cream cheese scrambled eggs. No thanks. Make sure you just use the yolk. You’ll layer the muffin batter and the cheesecake filling into the muffin liners. 1 layer muffin batter, 1 layer cheesecake, 1 layer muffin batter. It’s ok if some of your cheesecake filling is visible on the top or on the sides. That’s how you get pretty cheesecake swirls peeking out all over.

Finally? The streusel. The streusel is simple: brown sugar, flour, cinnamon, and melted butter. Sprinkle the buttery brown sugar streusel on top of the muffins before going into the oven. You’ll want to gently press it down into the batter so it won’t fall off the sides as the muffins are rising.

Pumpkin muffins filled with cream cheese filling and topped with sweet cinnamon brown sugar streusel!

I’m still not sure which part of the muffin I like the best. There’s just so much to love; every layer has a different texture and taste. A moist and flavor-packed tender pumpkin muffin, generously spiced and lightly sweetened with brown sugar. And the cheesecake! Tangy, yet sweet ripple of creamy goodness. Mmm. Oh! And the buttery slightly crunchy crumbles on top make the perfect finishing touch. I could eat the streusel with a spoon and be content. I just can’t choose. I want it all.

They pair wonderfully with a steamy cup o’ joe, make an excellent 4pm snack, and are perfectly acceptable to squeeze in right before midnight.

It may look like a lot of little ingredients, but most of them are repeated throughout each layer. Start baking!

Follow me on Instagram and tag #sallysbakingaddiction so I can see all the SBA recipes you make. 

Pumpkin Cheesecake Muffins

Super-moist spiced pumpkin muffins stuffed with cheesecake filling and topped with brown sugar cinnamon streusel.

Ingredients:

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 (measured correctly)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 and 1/2 teaspoons ground cinnamon
  • 1 teaspoon pumpkin pie spice1
  • 2/3 cup (133g) packed light or dark brown sugar2
  • 2 large eggs
  • 1 cup (227g) pumpkin puree
  • 1/2 cup (120ml) vegetable oil (or canola, or melted coconut oil)
  • 1/3 cup (80ml) milk
  • 1 teaspoon vanilla extract

Cheesecake Filling

  • 6 ounces (168g) cream cheese, softened to room temperature
  • 1 egg yolk
  • 1 teaspoon vanilla extract
  • 3 Tablespoons (36g) granulated sugar

Directions:

  1. Preheat oven to 425°F (218°C). Line two muffin sheets with 14 liners or spray with non-stick spray. Set aside.
  2. Make the crumb-topping first: Add the brown sugar, flour, and cinnamon to a small bowl and mix until combined. Add the melted butter and mix until crumbs form. Set aside.
  3. Make the pumpkin muffins: In a large bowl, toss the flour, baking powder, baking soda, salt, cinnamon and pumpkin pie spice together until combined. Set aside. In a medium bowl, whisk the brown sugar and eggs together until combined. Whisk in the pumpkin, oil, milk, and vanilla. Pour the wet ingredients into the dry ingredients and stir until just combined. Do NOT overmix the batter.
  4. Make the cheesecake filling: In a medium bowl, beat the cream cheese with an electric handheld (or stand) mixer on medium-high speed until creamy. Add the egg yolk, vanilla extract, and sugar. Beat until combined.
  5. Spoon 1 Tablespoon of pumpkin muffin batter into the muffin cups. Layer with about 1 spoonful (not quite a full Tablespoon) of cheesecake filling, then another Tablespoon of muffin batter (or however much batter is needed to fill the cups all the way to the top). Yes, you will fill the muffin cups to the very top. Some cheesecake filling may poke out of the top or on the sides. Sprinkle each muffin evenly with crumb topping and press the topping down into the muffin so it sticks.
  6. Bake for 5 minutes 425°F (218°C) then, keeping the muffins in the oven, reduce heat to 350°F (177°C)3 and continue baking for another 15-16 minutes. The total time these muffins should be in the oven is around 20-21 minutes. Allow the muffins to cool for 10 minutes in the muffin sheet, then transfer to a wire rack to cool until ready to eat. Muffins taste best on the same day, though they may be stored covered tightly at room temperature for 3 days or in the refrigerator for 5 days.
  7. Make ahead tip: For longer storage, freeze muffins for up to 3 months. Allow to thaw overnight in the refrigerator and heat up in the microwave if desired.

Recipe Notes:

  1. 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.
  2. I usually only use 1/2 cup brown sugar, but I find the pumpkin and spice flavor really excels with just a little more brown sugar. So, I prefer 2/3 cup.
  3. Why the initial high temperature? Like I do for most of my muffin recipes, you’ll 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, then the centers will bake during the lower temperature bake time.

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© Sally’s Baking Addiction. All images & content are copyright protected. Please do not use my images without prior permission. If you want to republish this recipe, please re-write the recipe in your own words, or link back to this post for the recipe. Some of the links above are affiliate links, which pay me a small commission for my referral at no extra cost to you! Thank you for supporting Sally’s Baking Addiction.

After you make these muffins, try these similar recipes next…

Cinnamon-Swirl Chocolate Chip Bread

Cinnamon-Swirl Chocolate Chip Bread

Favorite Pumpkin Oatmeal Cookies (soft, not cakey!)

These are my favorite pumpkin cookies! Filled with oats, chocolate, and cranberries!

Mini Cinnamon-Sugar Pumpkin Muffins

Mini Pumpkin Muffins

See more muffin recipes.

See more pumpkin recipes.

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

258 Comments

  1. 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…!?!

    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.

  2. 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 🙂

  3. 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!

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

  4. 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 🙂

  5. 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.

  6. 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! 🙂

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