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Home » Recipes » Sweets & Desserts

Healthy Double Chocolate Mini Cupcakes

By: Kathryn Doherty | Last Updated: Mar 4, 2025 | Published: Feb 8, 2016
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Easy, one-bowl healthy chocolate mini cupcakes are 100% whole wheat, low in sugar and have no butter or oil - and they are super fudgy and delicious!

A white plate with five chocolate mini cupcakes alongside colorful red napkins.


 

Happy Monday! My team lost the Super Bowl yesterday. Such a bummer.

So today, I’m moving on and it's all about Valentine’s Day!

My kiddos are on the young side still, so while we love to indulge around holidays, I do try and keep it on the healthier side.

(Plus, they have endless preschool parties and treats from grandparents and get plenty of sugar and sweets as it is.)

But of course we gotta have some chocolate this month!

And so we've been making these healthy double chocolate mini cupcakes as a sweet treat!

(Another favorite for little ones is this toddler Valentine's Day snack mix!)

Close up of double chocolate mini muffins on a small white plate with chocolate chips scattered nearby.

These little bites have been a big hit at our house. I mean, does it get better than cupcakes? Even bite-sized ones?

Not for my 4-year-old daughter it sure doesn't!

And these unbelievably soft, light, chocolate-loaded cupcakes, well, these make mama happy too.

They are 100% whole wheat, low in sugar and don’t have any butter or oil.

Plus, they are so sweet that you don’t even need icing. (Of course, feel free to add some if you'd like!)

All around, it's a much healthier version of cupcakes. And you better believe I popped a couple myself!

Close up of double chocolate mini muffins on a small white plate with chocolate chips scattered nearby on colorful cocktail napkins.

Also, just one bowl needed. So stinking easy.

So you won’t mind making a second batch 3 days after the first one has been devoured.

Oh, and they are vegan-friendly as well. Just use soy milk and vegan chocolate chips if needed.

Oh, and in case you need some, I use mini muffin pans like this all the time.

Healthy double chocolate mini cupcakes baked in a mini muffin tin

And if you are like me and love some healthy chocolate recipes, here are a few of our other favorites.

Healthy chocolate chip muffins are great anytime of day - for an afternoon snack, for a late night dessert and even for a fun breakfast!

Speaking of chocolate at breakfast, check out these whole wheat chocolate baked donuts and these healthy chocolate pancakes.

Or try this gluten-free and vegan-friendly 5-minute healthy chocolate pudding.

Healthy double chocolate mini cupcakes on a white plate with one picked up
Healthy double chocolate mini cupcake with a bite taken out

Back to these mini chocolate cupcakes though. Just look at that above! So very fudgy!

Last thing, let's talk about how to store these.

I recommend storing these little cupcakes in the fridge after the first day. (I actually like them cold so I keep them in the fridge once they’re cooled.)

They freeze well, too, if you want to get the extras out of sight so you don’t eat.them.all. Just place in a freezer-safe ziplock bag, label and date it, and freeze for up to 4-5 months.

Whether you make these for Valentine's Day or just to satisfy the must.have.chocolate feeling, I hope you enjoy these super chocolatey mini cupcakes!

XO,

Kathryn

Five double chocolate mini cupcakes on a small white plate with chocolate chips scattered nearby.
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4.09 from 12 votes

Healthy Double Chocolate Mini Cupcakes

Easy, one-bowl healthy double chocolate mini cupcakes are 100% whole wheat, low in sugar and have no butter or oil - and they are super fudgy!
Prep Time10 minutes mins
Cook Time15 minutes mins
Total Time25 minutes mins
Yield: 30 mini cupcakes

Ingredients

  • ¾ cup whole wheat flour, see notes
  • ½ cup granulated sugar
  • ¼ cup cocoa powder
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon salt
  • 1 cup unsweetened applesauce
  • ½ cup milk of choice
  • 2 teaspoons vanilla
  • ¾ cup semisweet chocolate chips
  • 1 extra teaspoon whole wheat flour

Instructions

  • Preheat the oven to 350. Spray a mini muffin tin pan with cooking spray and set aside.
  • Mix the flour, sugar, cocoa powder, baking powder, baking soda and salt in a large bowl until well combined.
  • Make a well in the center and add the applesauce, milk and vanilla. Stir until just combined.
  • Toss the chocolate chips with the extra flour (this helps keep the from sinking in the batter and sticking to the bottom of the muffin tins). Fold the chocolate chips into the batter.
  • Fill your mini muffin tins. Each muffin cup should be about ¾ full.
  • Bake at 350 for 14-16 minutes, until done.
  • Let cool completely in pan before turning out. (Otherwise the chocolate chips can stick to the muffin pan instead of to the cupcakes. Sad.)

Notes

Flour: I use white whole wheat flour but you can use whole wheat flour or all-purpose flour if you prefer.
Vegan: You can make these mini cupcakes vegan by using a milk substitute and vegan chocolate chips.
For full-size cupcakes, fill the muffin tins with paper liners and spray with cooking spray. (These don’t have butter or oil so they can stick really easily.) Bake the cupcakes at 350 for 22-24 minutes, until done. Let cool before removing. Makes 10 full-size cupcakes.
You can also split the batch and make 6 big cupcakes and 12 mini cupcakes.
Storage: Store leftovers in a covered container in the refrigerator after the first day. Or freeze in a freezer-safe ziplock bag or container for up to 4-5 months.

Nutrition

Serving: 1mini cupcakes | Calories: 55kcal | Carbohydrates: 9g | Protein: 1g | Fat: 2g | Saturated Fat: 1g | Polyunsaturated Fat: 0.1g | Monounsaturated Fat: 1g | Trans Fat: 0.004g | Cholesterol: 0.3mg | Sodium: 72mg | Potassium: 54mg | Fiber: 1g | Sugar: 6g | Vitamin A: 5IU | Vitamin C: 0.1mg | Calcium: 13mg | Iron: 1mg
Tried this recipe?Leave a comment below or follow me on Instagram @familyfoodonthetable and tag me in your photo!
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Reader Interactions

Comments

  1. Cheyanne @ No Spoon Necessary

    February 08, 2016 at 8:50 am

    Obviously my team lost too... sigh. It was not a pretty game that's for sure. Guess we need to stuff our face with these Mini cupcakes and eat our feelings, huh? Love that you always put a healthy spin on decadent dishes, Kathryn! DOUBLE chocolate cupcakes make mini and healthy?!? What's not to love?? Delicious! Cheers, my dear!

    Reply
    • Kathryn

      February 08, 2016 at 2:01 pm

      It was a sad loss... but a great season! And yes, I may be wallowing a little with chocolate today 🙂

      Reply
  2. April @ Girl Gone Gourmet

    February 08, 2016 at 10:01 am

    This was a crazy Super Bowl for us - I grew up in a bronco-loving family, but my boyfriend and I live in North Carolina now. I figured it was a win/win either way 🙂 Love these chocolately cupcakes - looks like your kiddos love them, too!

    Reply
    • Kathryn

      February 08, 2016 at 2:01 pm

      That's pretty cool - you win either way with this match-up!

      Reply
  3. lisa @ garlicandzest.com

    February 08, 2016 at 10:03 am

    These cupcakes look so moist! I'm sold. I like the smaller version too - like a quick one bite snack -- I don't feel guilty at all!

    Reply
    • Kathryn

      February 08, 2016 at 2:02 pm

      They really are super soft and moist - it's all the applesauce holding them together! Glad you love a bite-size treat too!

      Reply
  4. Willow | Will Cook For Friends

    February 08, 2016 at 11:15 am

    These sound so. freakin. good! Almost like brownies in little muffin form. I'll take a dozen, haha!

    Reply
    • Kathryn

      February 08, 2016 at 2:03 pm

      Yes, they are like little brownie bites! And I'm with you on a dozen 😉

      Reply
  5. Jenn

    February 08, 2016 at 11:19 am

    These little mini cupcakes looks delightful! I love the mini size...kids are still getting a treat, but it's nice control of portion size!

    Reply
    • Kathryn

      February 08, 2016 at 2:04 pm

      Thanks Jenn! Yes, I like the portion control part of these - for the kiddos and for me!

      Reply
  6. Sonal

    February 08, 2016 at 1:50 pm

    Our team won and won good...no no not trying to rub it in but just saying 😜...just kidding!!
    These double chocolate cupcakes are perfect for Valentine and any day!
    More admiration for you for not giving into the candy demands..

    Reply
    • Kathryn

      February 08, 2016 at 2:07 pm

      Haha, congrats on your win! I'm bummed but we had an awesome season so I'm holding my head high and still saying Go Panthers! These little chocolate babies are certainly helping me feel better, too. 😉

      Reply
  7. Matt @ Plating Pixels

    February 08, 2016 at 6:42 pm

    Gotta love extra chocolate. Since these are mini I'd totally eat a dozen and feel fine about it 😉

    Reply
    • Kathryn

      February 08, 2016 at 8:22 pm

      Haha, I like your style Matt 🙂

      Reply
  8. Sarah and Laura @ Wandercooks

    February 08, 2016 at 7:14 pm

    Ohhh you had us at chocolate! Looks so easy and delicious!

    Reply
    • Kathryn

      February 08, 2016 at 8:24 pm

      Easy and chocolate and - bonus! - healthy - ALL good things in my book 🙂

      Reply
  9. Patricia @ Grab a Plate

    February 08, 2016 at 8:31 pm

    At least your team was in it! Sorry for the loss, though (my hometown team -- Cleveland Browns -- is so far removed, and my adopted home team -- AZ Cardinals -- came really close)! These looks so good! Love the "double chocolate" part -- yum!

    Reply
    • Kathryn

      February 09, 2016 at 1:48 pm

      It was excited just to have our team go 🙂 And yes, double chocolate is always a good thing! 🙂

      Reply
  10. Shreyashi

    February 08, 2016 at 11:14 pm

    Hey Kathryn,
    The cupcakes looked great. I like how you ration candy for your kids. Kids these days are too hopped up on sugar anyway.
    Coming to the recipe, the use of applesauce is genius. I always love it when people use applesauce for baking.

    Reply
    • Kathryn

      February 09, 2016 at 1:50 pm

      Thanks! Agreed on the candy front. They still get it so I don't feel the need to add to it at all! And agree again - I love how healthy, light and moist applesauce makes baked goods 🙂

      Reply
  11. Adina

    February 09, 2016 at 5:15 am

    Such pretty muffins, my two would love them too.

    Reply
    • Kathryn

      February 09, 2016 at 1:51 pm

      Thanks Adina!

      Reply
  12. Lisa @ Chocolate Meets Strawberry

    February 09, 2016 at 5:39 am

    Looks like you made M very happy indeed with these little gems, Kathryn! That's one happy, chocolately smile right there! These muffins have my name all over them, too. This week has been a serious muffin frenzy in our house! I've already made two batches and it's only Tuesday! So we've been having muffins for breakfast, morning tea, afternoon tea and dessert. The best bit? We just don't get sick of them! These fudgy, chocolately ones will be next on my list of muffiny things to devour 😀 Pinned!

    Reply
    • Kathryn

      February 09, 2016 at 1:53 pm

      Girl loves her some chocolate! Must get it from me 😉 Hope you love them, too!

      Reply
  13. Kate @ Framed Cooks

    February 09, 2016 at 7:34 am

    Oh my gosh, that cute FACE!!! Love that you have made chocolate healthier and still scrumptious. 🙂

    Reply
    • Kathryn

      February 09, 2016 at 1:54 pm

      Haha, thanks Kate!

      Reply
  14. Summer

    February 09, 2016 at 9:50 am

    M is such a little cutie pie! And those cupcakes look so yummy ♥

    summerdaisy.net

    Reply
    • Kathryn

      February 09, 2016 at 1:54 pm

      Aw, thanks Summer 🙂

      Reply
  15. karrie@TastyEverAfter

    February 09, 2016 at 10:17 pm

    That game was the worst! I was even rooting for the Panthers because I didn't want the Broncos to win. UGH!! On happier note, these cupcakes are delicious looking! One bowl and healthy? Can it be true? All I know is that M knows what's good and if she loves them, then I know I'll love them too 🙂

    Reply
    • Kathryn

      February 09, 2016 at 10:29 pm

      Right, Karrie? Such a let-down... but I'm trying to stay positive because it was an awesome season and, well, there's that at least. Anyway, M is definitely the ultimate taste tester and she highly approves of these little cupcakes -- and particularly their bigger counterparts 😉

      Reply
  16. Frugal Hausfrau

    February 19, 2016 at 3:17 am

    These would't be so healthy for me because I just KNOW i'd eat like 10 of them! lol! Thanks for sharing this with us on Throwback Thursday!

    Mollie

    Reply
    • Kathryn

      February 19, 2016 at 10:11 am

      Haha, I have that problem too 😉

      Reply
  17. Jen

    March 28, 2017 at 10:41 pm

    These are really delicious. My 2 year old is obsessed with chocolate and so I make these as a healthier option and call it "chocolate cake". He LOVES them!

    Reply
    • Kathryn

      March 29, 2017 at 7:46 pm

      Haha, so glad to hear they are a hit with your little boy! Thanks for sharing! 🙂

      Reply
  18. Ifa

    November 18, 2018 at 6:45 pm

    Hi Kathryn!
    I’m a healthy baker newbie lol!
    Glad that i found your wonderful website here 😍
    I’d like to ask something (well idk if my question will be out of topic or not but let me just ask then)

    Ok, can i sub the baking powder to yeast as i used to bake doughnuts with a dry yeast instead of using baking powder?
    I haven’t tried to bake whole-wheat flour with yeast either but before i dunk my batter into my trash can let me just waiting for your reply 😂

    Thank you so much & Have a wonderful night there ❤️🙏

    Reply
    • Kathryn

      November 19, 2018 at 8:29 am

      Hi there - so glad you found me! Unfortunately, I don't think yeast would be a good substitution here. It would likely throw off the chemical mix and mess up the cupcakes. I'd stick with baking powder. Hope that helps!

      Reply
  19. Sue

    July 28, 2020 at 5:07 pm

    Is there any substitution for the applesauce?

    Reply
    • Kathryn Doherty

      July 29, 2020 at 7:13 am

      Hi Sue! You could try using part extra milk and part melted butter or canola oil in place of the applesauce. Would love to hear how it goes if you try it. 😊

      Reply
4.09 from 12 votes (12 ratings without comment)

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Hi there! I’m Kathryn Doherty, a cookbook author, mom of two, and devoted food and home cooking nut. I’ve got lots of easy recipes to help you get delicious food on the table for your family!

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