Applesauce Cupcakes with Cream Cheese Frosting

by Heidi @ Food Doodles on November 20, 2015

Soft, moist applesauce cupcakes made with 100% whole wheat flour (or AP flour) – but you wouldn’t know it because they’re so delicious! Buttery and perfectly spiced and topped with the greatest lightened up cream cheese frosting using Greek yogurt.

Do I have a special treat today!  These cupcakes are amazing!

I’m not just saying that, they really are.  It took me a couple tries to get the recipe just right and it really is perfect.

The applesauce makes them super moist and makes the cupcakes taste so bright!  And those spices…  Mmmm!  These applesauce cupcakes taste like fall!


Now don’t even get me started on this frosting.  I’ve used it before on this super delicious carrot cake, and have not gotten it out of my head since.

It’s obviously far lighter than a typical cream cheese frosting for starters, but it is the best!  I love it!

It’s a little thinner than a regular cream cheese frosting, but it does not run or drip, it’s the perfect thickness.  The only problem is that it should probably be kept in the fridge.

I recommend frosting these applesauce cupcakes before serving, otherwise you’ll have to store your cupcakes in the fridge.  I find storing baked goods makes them seem drier than they actually are, so I don’t really recommend keeping them in the fridge, but I’m saying that with some in the fridge right now.  They’re still yummy 🙂


You’ll notice something a little bit different in my recipe, and it’s something I should have done a long, long time ago.  I’m almost even embarrassed to say it…  I’ve finally started using weight measurements for flour.

I will of course still provide the cup measurement as I measure it, but if you’re having a problem with your baking, there’s a 99% chance it’s a problem with measuring flour.

There’s an incredible amount of room for error when using measuring cups.  If you love baking I recommend getting a kitchen scale, they’re inexpensive and I use one all the time even for things other than baking.

It’s very handy.  Oh, and I will be going back and changing old recipes but only after I test them to make sure they’re 100% accurate.

For now please enjoy these applesauce spice cupcakes!


Applesauce Cupcakes with Greek Yogurt Cream Cheese Frosting
Prep Time
10 mins
Cook Time
20 mins
Total Time
30 mins
Course: Dessert
Servings: 12 cup cakes
Author: Heidi @ Food Doodles
  • 1/2 cup salted butter softened
  • 3/4 cup brown sugar packed
  • 2 large eggs
  • 2 teaspoons vanilla
  • 1 cup applesauce scant
  • 1 1/2 cups (187g) white whole wheat flour (or all-purpose flour)
  • 1/4 teaspoon baking soda
  • 1 1/2 teaspoon baking powder
  • 1/2 teaspoon salt
  • 2 teaspoons cinnamon
  • 1/4 teaspoon nutmeg
  • 1/4 teaspoon cloves
  • 1 Recipe Greek Yogurt Cream Cheese Frosting recipe below
  1. Preheat oven to 375 degrees Celsius. Prepare a muffin tin by lining with paper liners or lightly greasing with non stick spray.
  2. In a bowl beat the butter until soft and fluffy. Add the brown sugar and beat again until fluffy. Add the vanilla and eggs and beat in until combined, one at a time. Add in the applesauce and mix until just combined.
  3. In a small bowl stir together the flour, baking soda, baking powder, salt, cinnamon, nutmeg and cloves. Add the dry ingredients to the wet ingredients and beat just until combined.
  4. Divide evenly among the 12 muffin cups. Place in the oven and bake for 17-19 minutes until a toothpick comes out clean and cupcakes are beginning to turn golden.
  5. Remove from the oven and let cool in the muffin tin for 5 minutes before removing and placing on a cooling rack.
Recipe Notes

Make sure you measure just slightly under 1 C of applesauce, especially if using a thinner store bought applesauce. I use a full cup of my homemade applesauce since I like mine a little thicker than typical store bought applesauce is.


Greek Yogurt Cream Cheese Frosting
Prep Time
5 mins
Total Time
5 mins
Course: Dessert
Author: Heidi @ Food Doodles
  • 3 oz cream cheese
  • 1/4 cup plain Greek yogurt
  • 1 teaspoon vanilla
  • 1/2 tablespoon lemon juice
  • 2 1/2 tablespoons honey
  1. With a hand blender whip the cream cheese until soft. Add all the other ingredients and beat until smooth.
  2. With a food processor simply add all the ingredients and blend until smooth.
  3. Frost cupcakes or cake just before serving as this frosting should be kept in the fridge.


Leave a Comment

{ 10 comments… read them below or add one }

1 Angela @thechewylife November 22, 2015 at 11:35

I totally agree with you about using the kitchen scale; it makes things exact so that baked goods can turn out consistently delicious 🙂 Btw, I love using honey in frosting! So delicious 🙂


2 Heidi @ Food Doodles November 27, 2015 at 21:43

Yes, absolutely! And honey is so good, especially in frosting 🙂 Thanks Angela!


3 Bethany @ Athletic Avocado November 21, 2015 at 12:50

Im super stoked about using greek yogurt for the frosting! A fantastic idea to cut calories! Great recipe;)


4 Heidi @ Food Doodles November 27, 2015 at 21:44

It works so well! I love it so much I use this frosting recipe all the time 🙂 Thanks so much Bethany!


5 Teresa November 20, 2015 at 20:23

It’s such a good idea to weigh flour, isn’t it? These sound wonderful!


6 Heidi @ Food Doodles November 27, 2015 at 21:45

Yes it is! So embarrassed that I’m just starting to do this now! Thank you Teresa! 🙂


7 Lily @GastroSenses November 20, 2015 at 12:00

I’m happy to be hit with a delicious looking recipe like this! I love cupcakes a lot and this easy and healthy version sounds perfect!


8 Heidi @ Food Doodles November 27, 2015 at 21:46

Thank you Lily!


9 Charlotte Moore November 20, 2015 at 05:52

I think I would like these without frosting. I am not one for cream cheese. Thank goodness!!! One less thing not to worry about the calories.


10 Heidi @ Food Doodles November 27, 2015 at 21:47

Haha, yes, I guess so! My kids were eating these without the frosting too, they’re really yummy even on their own 🙂


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