If you are looking for a simple fall baking recipe, try this recipe for apple cupcakes with cream cheese frosting. The cream cheese frosting is not too sweet and very thick and pipeable. The cupcakes are moist and flavoured with apple butter and fall spices.

Apple butter is my secret ingredient for adding a strong, highly concentrated apple flavour to baked goods without adding any water to a recipe. It's a much more efficient way of adding apples without diluting flavour or messing with cake batter ratios, thus avoiding gummy textures that can come from adding fresh chopped fruit.
I've baked with apple butter to flavour apple cakes— like in this apple butter cake recipe; in scones—slathered inside to make the most delicious apple pie scones; and I've also used it in pie filling in this gorgeous apple butter pie, which makes a great alternative to Thanksgiving pumpkin tarts and maple apple pie.
These mini spiced apple cupcakes are flavoured with apple butter and cinnamon for a truly fall flavour, and topped with a cream cheese frosting that tastes like cheesecake. Yes, I really did pipe dollops of frosting that are practically the size of the cupcakes themselves. You will understand why when you make this frosting.
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Ingredients and Substitutions
These moist apple cinnamon cupcakes with cream cheese frosting are made from simple ingredients that you likely have on hand. Still, there are a few things to note:
- butter—this recipe was developed with unsalted butter. If you prefer to use salted butter, you may have to adjust the amount of salt added to ensure the apple cakes aren't too salty.
- flour—I bake with bleached all-purpose flour, but unbleached should work too and give similar results.
- salt—I bake with Diamond Crystal fine Kosher salt. If using regular table salt, add half the amount to avoid the cupcakes being too salty.
- brown sugar—you can use light or dark brown sugar, or even regular white sugar (though the cakes won't be as flavourful as with brown sugar).
- apple butter—this is not to be confused with apple sauce! Apple sauce has much more water and may make the cupcakes too wet or gummy, and hard to bake through properly. Use apple butter! You could also replace the apple butter with pear butter or pumpkin butter.
- cream cheese—use full-fat cream cheese sold in blocks, not whipped or spreadable cream cheese. The texture of the frosting won't be the same with cream cheese spreads.
Please see the recipe card for a full list of ingredients and exact quantities.
How To Make Apple Spice Cupcakes
To make these mini apple cupcakes quickly and easily, we use the two-bowl mixing method, like many muffins and quick breads. Here's how to make these spiced apple cupcakes:
Step 1—Start by browning the butter in a small saucepan (image 1) so that it can cool before you make the spiced apple cupcake batter. Please read about how to make brown butter if you've never made it.
Step 1—Once the brown butter has cooled, you can whisk together the dry ingredients (image 2) separately from the wet ingredients (image 3) before combining them to make a smooth batter.
Step 3—I baked the cupcakes in mini muffin pans lined with mini cupcake liners (image 4), but you could also make full size cupcakes.
Step 4—After the cupcakes have cooled, top them with thick cream cheese frosting and garnish with graham cracker crumbs (image 5).
Tip: Remember to make the best cream cheese frosting, you need to first mix the butter and icing sugar before adding the cream cheese. Read all about thick cream cheese frosting with less sugar if you've never made it this way before!
Tips For Thick Cream Cheese Frosting That Is Stable And Pipeable
Without resorting to adding an excess amount of icing sugar, to make a thicker cream cheese frosting that can be used to frost a cake or decorate cupcakes, the solution is simple: change the order you mix your ingredients in:
Step 1: Cream the butter with the icing sugar first, thereby coating all the little sugar molecules with fat (I have no proof that this really happens, but my brain thinks it works like this, so bear with me!)
Step 2: Once the butter and icing sugar are well mixed, THEN you add in the COLD cream cheese. The sugar is coated with fat, therefore making it more difficult to draw out the moisture from the cold cream cheese. The cream cheese remains intact, and no water leeches out.
By following this mixing order, you can make a frosting with significantly less sugar. In fact, you end up with a frosting that tastes a lot like cheesecake, not overly sweet! At this point, you should be really excited for the recipe.
Once you have mastered this thick, pipeable cream cheese frosting recipe, you will see that it is so thick that you can use this cream cheese frosting to make layer cakes, like this berry chocolate cake with cream cheese frosting and this cardamom cranberry layer cake with cream cheese frosting, so you know it's good because this cream cheese frosting works great in layer cakes too without the risk of sliding layers and weeping frosting!
Frosting Alternatives
Another option for a thick cream cheese frosting is this white chocolate cream cheese frosting that is sweetened with melted white chocolate instead of icing sugar!
Apple Cupcake Baking FAQs
Cream cheese contributes double the moisture compared to butter. The icing sugar draws out that moisture and you end up with a soupy, runny, unstable cream cheese frosting, which is why many recipes have you add A TON of icing sugar to soak up that moisture. Read about how to make thick cream cheese frosting to see how changing the order you mix the ingredients allows you to create a thick frosting with half the sugar.
My favourite yogurt substitute is sour cream, either low-fat or full-fat.
Other Apple Recipes
Take advantage of fall when apples are at their peak (and more affordable too!). Try these other apple dessert recipes:
If you tried this recipe for the best apple cupcakes with cream cheese frosting (or any other recipe on my website), please leave a ⭐ star rating and let me know how it went in the comments below. I love hearing from you!
📖 Recipe
Apple Cupcakes with Cream Cheese Frosting
Ingredients
Apple cupcake ingredients
- 170 grams unsalted butter
- 287 grams bleached all-purpose flour
- 7.5 mL baking soda
- 7.5 mL ground cinnamon
- 2.5 mL Diamond Crystal fine kosher salt
- 250 mL apple butter
- 188 mL yogurt (2 % fat)
- 133 grams light brown sugar
- 2 large egg(s)
Frosting ingredients
- 250 grams unsalted butter room temperature
- 200 grams icing sugar divided
- 500 grams Philadelphia cream cheese (full fat, regular) cold
Optional for decorating
Instructions
To make the cupcakes
- Preheat the oven to 350 °F (175 °C). Line a 24 mini cupcake pan with mini baking cups (find them on Amazon.
- Brown the butter in a small saucepan until the foam subsides, the milk solids brown, and the butter gives off a delightful nutty aroma. If you've never done this before, read about how to make brown butter.
- In a large bowl, whisk together the flour, baking soda, cinnamon, and salt.
- In a separate bowl, whisk together the apple butter, yogurt, sugar, and eggs. Add this mixture to the bowl of dry ingredients and gently whisk to incorporate. When you just have a few dry lumps of flour left, add the melted butter, and finish mixing (with a wooden spoon, if necessary).
- Fill the liners ¾ full with the batter. I recommend using a ¾-ounce scoop (specifically this purple handled scoop on Amazon) for this.
- Bake the cupcakes for about 12 to 14 minutes, or until a cake tester inserted in the centre comes out clean. Let cool a couple minutes in the pan before carefully transferring to a wire rack. Line the pan again, then scoop and bake again until you've finished all the cake batter.
To make the frosting
- When the cupcakes are cooled, make the frosting. In the bowl of an electric mixer fitted with the paddle attachment, mix the softened butter with half the icing sugar. The mixture will be crumbly. Continue beating until creamy.
- Add all the cream cheese at once and beat it in. Then add the remaining icing sugar to sweeten/loosen up the frosting.
To finish
- Frost the cooled spice cupcakes by piping a generous dollop on each (I used a big 20 mm round tip, but you can just cut the end of a piping bag to the desired diameter). If using, top with a sprinkling of graham cracker crumbs just before serving.
Notes
- apple butter, not apple sauce! Apple butter has much less water than apple sauce and so they are not interchangeable.
- brown sugar in the cupcakes (light or dark works) but you could use white sugar
- yogurt though sour cream will also work (full fat or low fat)
- Diamond Crystal fine Kosher salt. If using table salt, add half the amount or the cakes may be too salty.
- Philidelphia cream cheese sold in blocks. Each block weighs 250 grams (0.55 lb). Do not use whipped or spreadable cream cheese in the frosting.
Rachel says
I am excited to try this recipe for thick cream cheese frosting. I am somewhat of a beginner, so would you mind telling me how long to mix in each step of the frosting recipe? Thanks.
Alisha Ross says
Definitely making these… wish the recipe was for fewer cupcakes so I don’t eat a dozen all by myself!!! They look amazing!
Janice says
Hah! I know the feeling. I made mini cupcakes so that I could share them with lots of people. Bring them to work or share them with your neighbours 😉
Bunny says
There's another reason Cream Cheese Frosting is soupy. Whipping cream cheese destroys the emulsifiers that bind it together. Once it's soupy, there's no saving it. Not even agar agar, a strong gelling agent (better than gelatin) can save it. I make my regular buttercream - 1/2 # butter, 1/2 c. Sweetex, 2 T. corn syrup, 1 t. agar agar, 1 t. vanilla, and 2 c. confectioners'. When It's all whipped, then I add 1 1/2 # soft cream cheese, and mix just barely to combine. It holds up great to frost and decorate with.
Marlycakes says
I like how you think! I just made a cream cheese frosting, and I creamed the butter and cream cheese together before adding the sugar. As you said, it was a loose frosting. Next time I'm going to try your method and see what happens! And also because it just looks so darned good!
Janice Lawandi says
Thank you! I hope you do get to try this cream cheese frosting recipe, and when you do, let me know what you think 🙂
Mardi Michels says
I am also a huge fan of Charlie Brown/ Peanuts - love your adult observations 🙂 Great recipe and excellent tips for the frosting.
Janice Lawandi says
Thank, Mardi! I wonder if kids these days like him as much as we do...
Mallory @ Because I Like Chocolate says
These look really good, love the pictures!
Janice Lawandi says
Thanks, Mallory!