Table of Contents
  1. Watch how to make these pumpkin cheesecake muffins:
  2. Have I convinced you to make this recipe?
  3. Pumpkin Cheesecake Muffins Recipe

I get it. Baking from scratch may seem like a lot of work. Not only do you have to make sure you have all the ingredients, but you also need to have the time to mix them together. Oh, and bake it yet to boot! Hold on, though… Before we go too far down that self-induced too-little-time pity party, you have to admit that when you bite into a warm, fresh-from-the-oven homemade baked good, you are in heaven. In this case, the pumpkin-spice-filled clouds burst open, and pumpkin cheesecake muffins floated down!

I love that when you bake your own goods at home, you can taste the quality ingredients that make up each bite, and you’re cognizant of the time and love that was put into each treat. I know baking doesn’t relax everyone as it does for me, but I also know everyone enjoys something delicious. These pumpkin cheesecake muffins are totally worth the effort, which in all honesty, isn’t really too much. And who doesn’t love anything pumpkin?!

Pumpkin cheesecake muffins sitting in basket fitted with linen towel sitting on wood board

The three layers of this muffin are pure perfection:

  • The pumpkin muffin base is moist and so flavorful.
  • The cheesecake layer has a bit of a soft texture, which is just what you want in this muffin.
  • The streusel topping is that perfect bit of crunch that perfectly caps off the whole experience.

If my (probably over the top) description thus far doesn’t convince you, just picture this. Imagine having the perfect treat to enjoy on a chilly fall morning with a steaming cup of coffee. Yes, please!

Pumpkin cheesecake muffins torn in half with cheesecake middle exposed held by hand with extra muffins and cooling rack in background
Doesn’t that cheesecake filling in the middle just look soooo good?! Trust me, it is!

Watch how to make these pumpkin cheesecake muffins:

YouTube video

Have I convinced you to make this recipe?

I hope you make this recipe and put some food on your table. Leave a comment and share a star rating so you can let others know how much you love this recipe. This helps show others that this is a recipe they, too, can make, enjoy, and love!

Pumpkin cheesecake muffins sitting on decorative wire cooling rack on wood board with basket full of muffins and towel in background all on gray slate surface with with background

Pumpkin Cheesecake Muffins

4.10 from 41 votes
Pumpkin is good on its own, but when it’s combined with a cheesecake filling, could it get any better?! Seriously, these pumpkin cheesecake muffins are the best and since they’re topped with a streusel topping, you just can’t go wrong!
Prep Time 30 minutes
Cook Time 23 minutes
Total Time 53 minutes
Servings 12 muffins


For the streusel topping

  • cup whole wheat flour
  • cup rolled oats
  • cup brown sugar
  • cup roasted pepitas (pumpkin seeds) or nut of choice, chopped
  • 1 tsp cinnamon
  • 5 tbsp butter

For the cheesecake filling

  • 6 oz cream cheese room temperature
  • cup sugar
  • 1 egg

For the pumpkin muffins

  • 1 cup pumpkin purée
  • ½ cup brown sugar
  • cup vegetable oil
  • 2 eggs
  • 2 tbsp molasses
  • 1 tsp vanilla extract
  • 1 cup flour
  • ½ cup whole wheat flour
  • 1 tsp baking powder
  • ½ tsp baking soda
  • 1 tsp cinnamon
  • 1 tsp ground ginger
  • ¼ tsp nutmeg
  • 1 tsp salt


  • Preheat oven to 350°F.

For the streusel topping

  • In a medium bowl, combine the whole wheat flour, oats, brown sugar, roasted pepitas, and cinnamon. Stir to evenly combine.
  • Cut butter into small pieces and work into the mixture until it looks like wet sand, as would be done for pastry dough. Set aside.

For the cheesecake filling

  • In a small bowl, whisk the cream cheese, sugar, and egg until smooth with no lumps.

For the muffin batter

  • Prepare the batter in a large bowl. Whisk the pumpkin purée and brown sugar until smooth.
  • Whisk in the eggs, oil, molasses, and vanilla until combined.
  • Add the flours, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Whisk until just combined and no streaks of flour remain.
  • Spray a 12-cup muffin tin with nonstick baking spray. Pour the prepared cheesecake batter into the muffin batter. Fold together sparingly until the mixture looks just swirled. Using a half-cup ice cream scoop, divide batter among the prepared muffin tins.
  • Top with the prepared streusel.
  • Bake in a preheated oven until puffed and set, 20-23 minutes.
  • Once baked, remove from oven and cool 15 minutes on a cooling rack.


Serving: 1muffinCalories: 418kcalCarbohydrates: 50.5gProtein: 6.2gFat: 22.2gSaturated Fat: 14.1gTrans Fat: 0gCholesterol: 86mgSodium: 333.1mgFiber: 2.8gSugar: 30.2g
Course Dessert
Cuisine American
Difficulty Intermediate
Method Baking

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I’m Kaleb! I'm not a chef, professional baker, landscaper, or designer, but I like to play each on Knollgate Farm. Come join me on my journey and let's learn together!

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  1. 5 stars
    My muffins are baking in the oven right now! They smell HEAVENLY and I cannot wait to see and taste the outcome. Thanks for sharing your videos and recipes. I’m exited to have found your site and try all the things fall you are posting about. You’re great in front of the camera and are sharing so many wonderful things with us. Next up, squash soup and the homemade apple butter. Can’t wait!

  2. 5 stars
    They were fabulous! Although it did take me about 33 minutes to bake through. Definitely be careful with how much your fold the cream cheese mixture in as it won’t show much if you overdo it even slightly. But they tasted wonderful!

  3. It’s a question really not a comment. Cream cheese usually comes in 8 oz bars, will it hurt the recipe if 8 oz. are used?

  4. Hi Wyse.
    Love your style of showing us your favorite recipes. You so pose for how everything comes out together. Your home is so welcome and peaceful… it is about that window and the high ceiling… magical to watch.
    I wanted to ask you if I could reduce the sugar or use stevia? Could make a small cake insist of cupcake?
    Do you have videos of roll/log cake with filling inside?
    Once again I enjoy you videos and recipes.
    Warm baking from the Caribbean.
    Rosa (Snoryea)

  5. 5 stars
    Because of dietary restrictions we used homemade plain chèvre from our Nubian goats instead of cream cheese and maple syrup instead of brown sugar and molasses and fresh ground einkorn flour, the rest the same, and they were delicious!

    Topping using maple syrup, coconut butter, and einkorn flr, oats, roasted nuts, cinnamon.

    1. I am wondering if gluten free flour blend would yield the same results. I am celiac so need to avoid gluten. Thoughts?

  6. In your recipe above you swirl the cream cheese mixture into the pumpkin flour mixture, in your video you layer it in. Any thoughts on that? ( mine are in the oven now, using the layering process)

  7. I bake for a little assisted living memory care home and will definitely make these in the very near future. I can tell this is going to be a five-star wonder.

    I just have to ask wherever did you find such a cute cooling rack?

  8. 5 stars
    I am from Port Hood, Cape Breton in Canada and have just made your pumpkin cheesecake muffins. They are delicious. My new favorite muffin. Thank you for sharing your recipes. I will definitely make these again.