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Chocolate Rainbow Cupcakes

5 from 21 votes

How to make kid friendly chocolate rainbow cupcakes from scratch. The recipe can even be vegan or gluten free, with no food coloring required!

Chocolate Rainbow Cupcakes

Magical rainbow cupcakes

If you’ve ever wondered what unicorns eat for dessert, now you know. It’s these homemade dark chocolate rainbow unicorn cupcakes.

The vibrant and delicious cupcakes are a perfect choice for birthday parties.

Or turn them into gender reveal cupcakes, swapping the rainbow filling with pink or blue. You can also make galaxy cupcakes. (See these Galaxy Donuts.)

They may look like plain and ordinary chocolate cupcakes on the outside… but just one alluring bite reveals the sweet magical rainbow filling hiding underneath!

You may also like these Sweet Potato Brownies

Unicorn Cupcakes Surprise Rainbow Filling

Chocolate rainbow cupcake ingredients

The cupcakes call for cocoa powder, flour, sugar, baking soda, salt, water, applesauce or yogurt, oil, pure vanilla extract, white or apple cider vinegar, rainbow unicorn filling, and optional mini chocolate chips.

If you do not have applesauce or yogurt, use an equal amount of mashed banana or roasted sweet potato puree.

I use a combination of regular unsweetened cocoa powder and Dutch process cocoa powder, because Dutch cocoa gives chocolate baked goods a classic brownie flavor. It should be readily available at most grocery stores but can be substituted with additional regular cocoa if you prefer.

The recipe works with white sugar, evaporated cane juice, or unrefined coconut sugar. For sugar free cupcakes, granulated xylitol will also work here.

Watch the rainbow unicorn cupcake recipe video – above

Rainbow Cheesecake Dip

How to make rainbow cupcakes

You can either prepare the rainbow filling ahead of time and store it in the fridge, or whip it up while the cupcakes are baking.

Preheat the oven to 350 degrees Fahrenheit, and line a muffin tin with liners.

Whisk the water, applesauce or yogurt, vanilla extract, and vinegar in a large mixing bowl. Let this mixture sit while you sift the dry ingredients in a separate bowl.

Pour wet into dry, and stir until just evenly combined. Smooth the cupcake batter into the prepared cupcake liners, going about two thirds of the way up.

Bake the tray on the center rack of the oven for twenty minutes. Or if you are making mini cupcakes in a mini muffin tin, bake for ten minutes.

When time is up, the cupcakes should be domed, with a toothpick inserted into the center coming out mostly clean. (See the video above for a visual.)

Let the cakes cool before adding the unicorn filling.

Kids Rainbow Birthday Cupcakes

How to fill cupcakes

You have a few options. The first way to stuff cupcakes is to add the filling to a pastry bag or a Ziploc with an icing tip placed in the corner and a small hole cut out. Squeeze the filling into the center of each cupcake through the bottom.

The second way is to use a spoon to cut out a piece of the cupcake top. Scoop the filling into the center, then smush the top piece back on. Hide the seam with frosting or melted chocolate or ganache.

These cupcakes taste even better a day after they are made, with a fluffier texture. Liners peel off easily after a day as well.

Star Unicorn Chocolate Cupcakes

Storing the unicorn cupcakes

Store the cupcakes, either on the counter or in the refrigerator, in a covered container. Leave a small opening so excess moisture does not get trapped.

After a day or so, it is best to refrigerate any leftover cupcakes for optimum freshness.

You can also freeze the cupcakes for up to two months. To ensure the filling retains its smooth and creamy texture, it is best to frost and fill the chocolate cupcakes after thawing, instead of before freezing.

Rainbow Unicorn Cupcakes

The recipe was adapted from my Vegan Chocolate Cupcakes and these Oreo Cupcakes.

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Chocolate Rainbow Cupcakes

These magical chocolate rainbow cupcakes are a perfect recipe for birthday parties.
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Yield 9 – 10 cupcakes
5 from 21 votes


  • 3/4 cup water
  • 1/4 cup applesauce or yogurt of choice
  • 1/4 cup oil
  • 2 tsp pure vanilla extract
  • 1 tsp white or cider vinegar
  • 1 cup spelt, white, or bob’s gf flour (Low carb option: Keto Cupcakes)
  • 3/4 cup sugar, unrefined if desired
  • 1/4 cup unsweetened cocoa powder
  • 2 tbsp Dutch cocoa powder or additional unsweetened
  • 1/2 cup mini chocolate chips (optional)
  • 1/2 tsp + 1/8 tsp salt
  • 1/2 tsp baking soda
  • 1 batch Rainbow Unicorn Dip
  • optional melted chocolate chips for the top


  • *The extra 2 tbsp cocoa can be Dutch or regular. I highly recommend Dutch for deeper chocolate flavor. Use regular unsweetened cocoa for the initial 1/4 cup.
    Preheat oven to 350 F. Line a cupcake pan. Whisk first 5 ingredients. Let sit at least 10 minutes, and sift all remaining ingredients in a new bowl while waiting. Pour wet into dry, stir just until evenly mixed, and smooth into the liners. Only fill up 2/3 of the way, because they rise a lot and you don’t want them to burst and sink in the middles (although if it happens, just hide with frosting!). Bake 20 minutes. Let cool. Filling can either be added by squeezing through a pastry bag inserted in the bottom of each cupcake or by using a spoon to cut out a piece of the top, add filling, smush the piece back on, and top with frosting or melted chocolate to hide the seam. Liners peel off easily if you serve the cupcakes the next day.
    View Nutrition Facts


Use any leftover filling to frost these Vegan Brownies.

Have you made this recipe?

Tag @chocolatecoveredkatie on Instagram

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Published on July 26, 2023

Meet Katie

Chocolate Covered Katie is one of the top 25 food websites in America, and Katie has been 
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Huffington Post, and 
ABC's 5 O’Clock News. Her favorite food is chocolate, and she believes in eating dessert every single day.

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  1. Alison Nicole says

    awwwww!!! I LOVE her!

    it was my dream to have a scottie when i was little. but Tilly’s pretty wonderful too! :o)

  2. Kristin says

    hi, i just found your blog recently by way of eatliverun. i love what i have read so far, so many good recipies i cant wait to try! we are neighbors, too, i live just north of dallas! do you go to smu?

  3. Billy says

    Nice picture. 🙂

    Thanks for adding me to your blogroll.

    If you’ve been vegan for seven years then you went vegan at 14. Is that right? That’s amazing. I’ve been vegan for just over six (went vegan at 19).

  4. Billy says


    I hope you and Chocolate Covered Vegan are able to meet up. That’s great when you connect with fellow vegans online!

  5. Ruby Red Vegan says

    ahh, those eyes and ears! they’re so full of expression! animals are awesome, seriously – they can express themselves with their ears!

    yay for the blogroll! i need to make one too, but i’d feel bad if i left someone out… kinda how i got with birthday parties in middle school. i stopped having them because i was never sure who to invite and who not to invite, out of fear of hurting feelings. oops, i guess there was also the “should i invite a boy factor?”. and now i got really off-topic. 🙂

  6. ChocolateCoveredVegan says

    Hey Kristin! I don’t see a blog link for you, so I hope you see this message here!

    Thanks so much for the sweet comments :o). And yes, I DO go to SMU! But my parents live northwest of Dallas… what part are you in?

  7. Kristin says

    Yeah.. I don’t have a blog 🙁

    I figured you probably go to SMU, since you live in Dallas! I have a few friends who may go there in the fall. I live northEAST of dallas. 🙂

  8. missblueberry says

    Your dog is just too cute! Your cupcakes look amazing – seriously you should open a shop. A poetry cupcake cafe? What do you say?

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