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Pumpkin Cupcakes with Cream Cheese Filling

If you’ve ever tried to make a pumpkin roll, you know how frustrating they can be. Just when you think you have it, boom. The little sucker breaks and you’re left with a cream cheese filled mess you try to cover with powdered sugar. It’s just sad. Instead of all that, take on these pumpkin cupcakes with cream cheese filling. All the same flavors, and none of that pumpkin roll headache. 

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Pumpkin rolls can be way to hard to make. All that waiting, cooling, rolling--and breaking. Make your life easier with all the same flavors in an easy to make pumpkin cupcake with cream cheese filling.

Pumpkin rolls are like time bombs (go look at mine–it has a crack in it). Bake that thing even one minute longer than you should and it will give you fits when you try to roll it. The next thing you know your face is flaming red, your sweating and telling yourself there’s a reason why you don’t cook.

But thank goodness for better options. A pumpkin cupcake with cream cheese filling is the exact same flavor without all that struggle. Because I struggle enough to remember where I left my car keys or if I unplugged the iron before I left the house. I don’t need any more to think about.

Soft, warm and totally soothing right from the oven, you can make these in just a few minutes. If you really, really wanted to cheat, you could use a spice cake mix from the store, add the cream cheese and crumble topping and bake them. They wouldn’t be pumpkin, but they’d still be good. Sometimes winners have to cheat.

Pumpkin rolls are stress. Say no to stress with all the same flavors and none of the worry with pumpkin cupcakes with cream cheese filling.

This recipe makes 24 cupcakes–the softest, spongiest, most moist little bits of sweet heaven you’ve put in your mouth this week. Well, maybe not but you can just keep your personal stories to yourself. This is a family blog people.

So go make yourself a big batch. Share them with someone you love or eat the whole pan by yourself–it doesn’t matter to me. They freeze well too so it’s fine to cool them and drop them in to a ziplock bag for storing. You can warm them in the oven when another craving (or last minute potluck) leaves you hanging.

Pumpkin rolls can be way to hard to make. All that waiting, cooling, rolling--and breaking. Make your life easier with all the same flavors in an easy to make pumpkin cupcake with cream cheese filling.

Pumpkin Cupcakes with Cream Cheese Filling

Why try to make a pumpkin roll when these pumpkin cupcakes with cream cheese filling take away all of the headache? Get my foolproof recipe here. 
Prep Time 12 minutes
Cook Time 18 minutes
Total Time 30 minutes
Servings 12 people
Author Rachel Ballard


For the filling:

  • 8 oz cream cheese softened
  • 1 cup powdered sugar

For the muffins:

  • 4 large eggs
  • 2 cups raw cane sugar coconut sugar, granulated sugar or maple sugar can substitute
  • 2 cups pumpkin puree or one 15 ounce can
  • cups avocado oil melted butter or vegetable oil can substitute
  • 3 cups all-purpose flour
  • 1 tablespoon plus 1 teaspoon pumpkin pie spice
  • 1 teaspoon salt
  • 1 teaspoon baking soda

For the crumble:

  • ½ cup raw cane sugar coconut sugar, granulated sugar or maple sugar can substitute
  • 5 tablespoons flour
  • teaspoons ground cinnamon
  • 4 tablespoons cold unsalted butter cut into pieces


  • Preheat the oven to 350.
  • In a small bowl beat the cream cheese and powdered sugar. Set aside.
  • In a large bowl mix the eggs, oil, pumpkin, and sugar. Set aside. 
  • Then in another bowl mix the flour, pumpkin pie spice, salt, and baking soda. No need to sift.
  • Slowly add the dry ingredients to the wet and mix until just combined.
  • Line or spray a muffin tin.
  • Add about a tablespoon of batter to the bottom of the muffin tin.
  • Scoop about a teaspoon of filling into the center of each muffin cup (or an amount a little larger than a quarter)
  • Cover with batter, about ¾ of the way up the muffin tin.

To make the crumble:

  • In a medium bowl, cut the cinnamon, sugar, flour and butter together with your fingers, a pastry cutter, or two knives until it resembles coarse crumbs. Sprinkle over each muffin. Bake for 18-22 minutes or until a toothpick comes out clean.


Calories: 121kcal
Tried this recipe?Tag us on Instagram @feastandfarm and hashtag it #feastandfarm
Course Breakfast, Dessert
Cuisine American

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  1. 5 stars
    Absolutely delicious! All the flavors are balanced so nicely. I accidentally whipped the cream cheese, so I had some batter left over. Thanks for a great recipe!

    1. Hi Joyce,

      My best suggestion would be to freeze them Joyce. Cupcakes can’t really hold out any other way. A couple of days–maybe up to three in an air tight container in the fridge might work but not a week. :/ –Rachel

  2. your recipe includes cinnamon in the instructions for the cake batter and the amount not list in the ingredients for the cake. The pumpkin pie spice has cinnamon in it. Are you adding more cinnamon??

    1. Hey Jan, It should be pumpkin pie spice in the batter and cinnamon in the crumble on top. Sorry about that–I’m glad you’re keeping an eye on me. I’ve fixed it in the recipe. 🙂 –Rachel

  3. How much nutmeg shall I use? The directions mention Nutmeg but, the ingredients don’t list it.
    Thank u

    1. Hey Desiree, You don’t need the nutmeg. This was actually an old recipe that I updated. It used to have several separate spices but the pumpkin pie spice covers it all. I just forgot to pull the nutmeg from the instructions. I’ve updated it now. Thanks for catching that. 🙂

  4. Rachel I love pumkin rolls too and i agree about the mess when i make them. What do you think about this idea…instead of baking them with the cream cheese inside, bake the cupcakes (minus the cream cheese) and insert the cream cheese inside each cupcake from the bottom using a cake decorating bag and large decorating tip after they have cooked and cooled. I thought about doing it this way but using a mini-muffin pan instead.

    1. Debra I think that’s a great idea, and you could most certainly do that. It may change the filling texture just slightly not to have baked it with the cupcakes, but I don’t think it will matter at all. Either way would work!

  5. What a great way to make pumpkin roll with kids minus some of the mess. My Daughter will love making these for Thanksgiving. Thanks for the idea!

    1. I think so too Krista! I love pumpkin rolls but I hate the mess. There’s just something miserable about putting powdered sugar all over my dish towels–haha! I hope your family enjoys the muffins. Happy Thanksgiving!

  6. I just made these and they’re wonderful! I made a little more extra crumb topping, other than that, followed the recipe exactly. I’m adding these to my permanent collection.

    1. I’m so glad you liked them Pam! I thought mine needed a little more topping and cream cheese, but I loved them too. They didn’t last long in our house. Thanks for letting me know about your success!–Rachel

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About the Author

Rachel Ballard, RN, BSN brings more than 20 years of professional nursing expertise to Feast and Farm. With a love for nutrient dense foods that support wellness, she works to distill complex health information and current trends into recipes that fuel the best version of yourself. Read more about Rachel here.