Chocolate Cherry Cupcakes {With Filling}

Soft and moist chocolate cherry cupcakes recipe, homemade with simple ingredients. Filled with maraschino cherry truffles and topped with fudgy chocolate frosting.

*Thank you Nielsen Massey Vanillas for sponsoring this post so that I can share this recipe with all of you. As always, all opinions are my own.*

I am really fond of Filled Cupcakes (Stuffed Cupcakes). That burst of flavor when you take your first bite is the best thing in the world. That blast is what inspired these cupcakes. Initially, I was thinking of using fresh cherries in them, but who can resist maraschino cherries? So, I used maraschino cherry juice in the batter and I stuffed a cherry in each chocolate truffle. If you are a fan of these flavor combinations, you should make these cupcakes ASAP! They have the perfect balance of sweet and tart flavors. They are also very soft, thanks to the use of Greek yogurt. On their own, these cupcakes are not too sweet. That’s why they pair so nicely with fudgy chocolate frosting that’s quite sweet. This Cherry Cake {With Cake Mix} also highlights this fruity cherry flavor very well.

Easy Maraschino Cherry Cupcakes With Chocolate Frosting on Peeled Wrapper

How to make easy chocolate cherry cupcakes recipe from scratch?

  1. Mix ingredients– This includes butter, sugar, eggs, extracts, yogurt and cherry juice.
  2. Whisk dry ingredients– Including the flour, cocoa powder, baking powder and baking soda.
  3. Combine mixtures– Don’t over-mix!
  4. Pour batter– Into cupcake liners.
  5. Bake– Until an inserted toothpick in the center comes out clean.
  6. Prepare the chocolate frosting– While cupcakes cool.
  7. Add chocolate truffle- By making a hole in the center of the cupcake.
  8. Decorate– With chocolate icing and a cherry.
Sliced Chocolate Cherry Cupcakes With Truffle Filling

Key ingredients

  • Flour- This should be all-purpose flour. No other flour yields the same results.
  • Cocoa powder– This should be unsweetened.
  • Butter– Unsalted is best.
  • Granulated sugar- This adds sweetness.
  • Greek yogurt– This adds moisture to cupcakes.
  • Maraschino cherry juice– This adds a boost of cherry flavor.
  • Eggs– They should be large and preferably at room temperature.
  • Vanilla extract– For flavor.
  • Baking powder and baking soda– These help the cupcakes rise.
  • Chocolate cherry truffles– These are added to the center of these treats after baking.

Speaking of ingredients, my latest discovery is Nielsen-Massey’s Tahitian vanilla extract. It has a wonderful fruity cherry flavor, which reminds me of flowers and Spring time! For today’s recipe, I used a combination of Tahitian and Mexican vanilla extracts. These two extracts worked together harmoniously to really enhance the overall flavor and aroma of these cupcakes!

Bottles of Neilsen Massey Extracts on White Background

Variations for maraschino cherry cupcakes

Use a larger piping tip– Since I am fond of cupcake decorating, I used the small star tip to make three layers of pretty chocolate swirls. You can just pipe one regular big swirl, if you like with Tip 1M. That’s simpler and easier.

Pair with another frosting– Such as Chocolate Cream Cheese Frosting, Chocolate Ganache Frosting {2 Ingredients}, or Chocolate Buttercream Frosting Recipe.

Try another filling– Like this How to Make Raspberry Pie Filling, How to Make Strawberry Pie Filling, or How to Make Blueberry Pie Filling.

Use fresh cherries and juice– If you are not fond of maraschino cherries.

Black Forest cupcakes– For these, replace the chocolate frosting with Homemade Stabilized Whipped Cream or American Buttercream Frosting Recipe.

Tips and techniques

What is a substitute for Greek yogurt? Sour cream makes a great substitute for these cupcakes.

Don’t over-mix batter– Because you will end up with dense “gummy” cupcakes.

Don’t over-bake cupcakes– They are done when an inserted toothpick in the center comes out clean. If you over-bake, cupcakes will be dry.

Use full fat Greek yogurt– This creates the best flavor and texture in the cupcakes.

Divide the work over a few days– Now, I will be the first to admit that these cupcakes take a bit longer to prepare but you can divide the work over a couple of days to make it less overwhelming, if you like.

The cupcake batter is really thick– Don’t worry about it. Just don’t over-mix!

Let the cupcakes rest for 10 minutes on the countertop– Because this resting time helps these cupcakes rise better.

All ingredients must be at room temperature– Because they blend together better and more smoothly.

Cool cupcakes before frosting– Because if you don’t, the frosting will melt and slide right off the cupcakes.

Use unsalted butter– Because this prevents the cupcakes from becoming too salty.

Use high quality ingredients– The better your ingredients, the better your food will taste. I never fully understood this bit of wisdom until I became obsessed with baking. I use the best quality of butter, cocoa powder, eggs, chocolate and extracts I can find. They are totally worth it and make a difference.

Closeup Shot of Chocolate Frosting Piping on Top of Cupcake

Storage of homemade cupcakes

Refrigerate– Leftovers can be stored in a sealed container for up to 3 days.

Freeze– Baked cupcakes, truffle filling and frosting can be stored in individual sealed containers for up to 1 month. When you are ready to enjoy these cupcakes, thaw to room temperature and assemble, as per instructions below.

Room temperature– These can be stored in a covered box or tray away from direct heart for about 1 hour.

More cherry desserts

Easy Chocolate Cherry Cupcakes With Chocolate Frosting on Peeled Wrapper
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Chocolate Cherry Cupcakes

Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes
Soft and moist chocolate cherry cupcakes recipe, homemade with simple ingredients. Filled with maraschino cherry truffles and topped with fudgy chocolate frosting.
Yield: 24 Cupcakes



Cherry truffle filling



  • In a mixing bowl, cream butter and sugar together until light and fluffy.
  • Then, add eggs and extracts and mix until just combined.
  • Add yogurt and cherry juice and mix again.
  • Now, in a separate small bowl, whisk together the flour, cocoa powder, baking powder and baking soda.
  • Dump the dry mixture into the wet mixture and mix until just combined. Don’t over-mix! The batter will be very thick.
  • Pour this batter into cupcake liners and let the tray sit on the countertop for 10 minutes.
  • Then, bake at 350 degrees F for 20 minutes or until an inserted toothpick in the center comes out clean.
  • While the cupcakes are baking, prepare the chocolate frosting.

Chocolate cherry truffles

  • Melt chocolate chips in a microwave-safe bowl.
  • Add condensed milk and vanilla extract and mix until you have a thick mixture.
  • Chill this mixture in the fridge for 45 minutes. Then, scoop out small portions of the mixture and roll them into little balls with a cherry stuffed in the center.
  • Place these truffles on a cookie tray lined with parchment paper and chill in the refrigerator for 30 minutes.
  • When the cupcakes have cooled down, use an apple corer or big piping tip to make a hole in the center of the cupcake.
  • Place a chocolate truffle in this hole.
  • Then, frost your cupcakes with chocolate icing and top it all off with a cherry. Enjoy!


  • Read all my tips above.
  • Leftovers can be stored in a sealed container in the fridge for up to 3 days. 


Calories: 279kcal, Carbohydrates: 42g, Protein: 4g, Fat: 10g, Saturated Fat: 6g, Cholesterol: 31mg, Sodium: 100mg, Potassium: 130mg, Fiber: 1g, Sugar: 31g, Vitamin A: 225IU, Vitamin C: 0.5mg, Calcium: 94mg, Iron: 1.2mg
Course: Dessert
Cuisine: American
Calories: 279
Author: Abeer Rizvi

4 comments on “Chocolate Cherry Cupcakes {With Filling}”

  1. I totally agree on using the best ingredients possible. And when the results turn out like this? Even better. I’m up for anything cherry.

  2. OMG. Seriously. I want them now. I was thinking about baking something for Valentine’s Day, but I wasn’t sure what, but now I know!5 stars

  3. These look so sweet and decadent. I cannot wait to try them!5 stars

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