Moist and Fudgy Chocolate Cupcakes


Last Updated on September 17, 2021. This post may contain affiliate links.  Please see my Disclosure Policy for more details.

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moist and fudgy chocolate cupcakes

These bakery-style made-from-scratch chocolate cupcakes are moist and fudgy with a rich chocolate flavor–Combine them with your favorite fillings and frostings and you have the only chocolate cupcake recipe you’ll ever need! From Peanut Butter Cup Cupcakes to Chocolate-Covered Strawberry to Double Chocolate, you can mix and match the favorite flavors that we were known for at Amycakes Bakery.

How to Make Extra Moist Chocolate Cupcakes

This recipe starts with the base cake recipe in my moist Triple Chocolate Ganache Bakery-Style Cake, but I’ve found that cupcake recipes require additional moisture to stay extra-moist. In Seven Secrets to Baking Incredibly Moist Cakes Every Time, I talk about these ingredients in detail:

  • The acid in Buttermilk breaks down the gluten in the cake batter, providing a more tender cake.
  • Vegetable Oil allows the cupcake to stay softer and moister than butter alone.
  • Instant Clearjel (my favorite secret bakery ingredient) allows the cupcakes to retain more moisture while keeping a light texture. Also called “Instant Clear Jel” or “modified cornstarch,” it is needed for the moisture and structure of these cupcakes. If you can’t get your hands on it in time, you can check out my suggested substitutes for Instant Clearjel (though I may try to persuade you that you need it in your pantry).

Making Chocolate Cupcakes with a Rich Chocolate Flavor

The batter of chocolate cupcakes is made with both cocoa powder (I use Hershey’s) and melted chocolate chips (I use Nestle). The result is a fudgy and extra-chocolatey cupcake. These cupcakes use the Two-Bowl method, which means no mixer is required to make the cake batter. The video in my Triple Chocolate Ganache Cake recipe shows me making a very similar Two-Bowl method cake batter.

I like to use a two-ounce scoop to scoop out my cupcakes so they are uniform, and I’ve found that darker nonstick cupcake tins provide a more uniform bake with the best rise. For the beginning of the bake, we’ll bake them at 350 degrees to help them rise, and then we’ll reduce the temperature to 300 degrees without opening the oven. This keeps them moist and prevents them from over-baking around on the edges.

Mix and Match your Chocolate Cupcake Fillings and Frostings

Suggested Chocolate Cupcake Flavors

Moist and Fudgy Peanut Butter Cup Cupcakes
Peanut Butter Cup Cupcakes: Chocolate Cupcakes with Peanut Butter Buttercream. Fill with Chocolate Ganache for Peanut Butter Fudge Cupcakes!
moist chocolate cupcakes chocolate covered strawberry
Chocolate Covered Strawberry Cupcakes: Chocolate Cupcakes with Strawberry Compote filling and Chocolate Buttercream.
Double Chocolate Cupcakes: Chocolate Cupcakes with Chocolate Buttercream. Fill with Chocolate Ganache for Triple Chocolate Ganache Cupcakes!
Chocolate Tuxedo Cupcakes: Chocolate Cupcakes with Chocolate Ganache filling and Vanilla Buttercream.

I sure hope you enjoy these recipes! Which flavor will you be trying? 🙂

Thanks for Reading. ❤️

Amy's Signature
5 from 28 votes

Moist and Fudgy Chocolate Cupcakes

These bakery-style made-from-scratch chocolate cupcakes are moist and fudgy with a rich chocolate flavor–Combine them with your favorite fillings and frostings and you have the only chocolate cupcake recipe you'll ever need! From Peanut Butter Cup Cupcakes to Chocolate-Covered Strawberry to Double Chocolate, you can mix and match the favorite flavors that we were known for at Amycakes Bakery.
If you have a kitchen scale, please select grams above the ingredients for the most accurate results. If you don’t have a scale, no worries!–just be sure to “spoon and level” your flour and cocoa, and to fully-pack your brown sugar into its measuring cup.

Watch the Recipe Video:

Yields 19 cupcakes
Prep Time 10 mins
Cook Time 16 mins
You may double the recipe by selecting 2x.
Select “grams” if you have a kitchen scale for more accurate baking.


Dry Ingredients

  • 1 ¼ cup + 2 Tbsp All-Purpose Flour (I use Gold Medal)
  • 1 ½ tsp Baking Powder
  • 1 tsp Baking Soda
  • ¾ tsp Salt
  • 2 Tbsp Instant Clearjel (A bakery ingredient you can use at home–see Note #1)
  • ¼ cup Unsweetened Cocoa Powder (I use Hershey's)
  • ½ cup Sugar
  • ½ cup packed Brown Sugar

Wet Ingredients

  • 2 large Eggs
  • ¾ cup + 2 Tbsp Buttermilk
  • ¼ cup Brewed Coffee
  • ½ cup Vegetable Oil
  • 3 Tbsp Dark Corn Syrup (or use light corn syrup)
  • 1 ½ tsp Vanilla Extract

Chocolate Butter Mixture

  • ¾ stick(s) (3 oz) Salted Butter
  • ¼ cup + 1 Tbsp Semi-Sweet Chocolate Chips (I use Nestle)

Your Choice of Cupcake Filling (optional):

Your Choice of Decorations (optional)



Turn Instruction images ON or OFF

Make Chocolate Cupcakes

  • Preheat oven to 350 degrees. Fill cupcake tins with 19 cupcake liners.
  • Using a sifter or fine mesh strainer, sift the first seven Dry Ingredients into a large bowl, then add brown sugar. Whisk until well blended. If you see any large brown sugar clumps, break them up and blend them in with your fingers.
  • Combine Wet Ingredients in a separate large bowl and whisk until smooth and well-blended.
  • Melt salted butter in the microwave (or over the stove) until just melted. Avoid overcooking. Add semi-sweet chocolate chips and whisk until melted and smooth (Whisk for 30 seconds to 1 minute–the heat from the melted butter plus the whisking will melt the chips).
  • Pour Wet Ingredients into Dry Ingredients and whisk until incorporated. Pour Chocolate Butter Mixture over batter and whisk until smooth and lump-free. (A few teeny brown sugar lumps are ok and will dissolve as it bakes).
  • Using a 2-oz scoop or 1/4 cup measuring cup, scoop batter into prepared cupcake tins.
  • Allow tins to set for 5-10 minutes before putting it in the oven. This will give time for the instant clearjel to thicken the cake batter before it bakes, allowing for a better rise.
  • Bake in the middle or top rack (avoid bottom rack) of the preheated 350-degree oven for 8 minutes. Without opening the oven, turn the temperature down to 300 degrees and bake for another 8-10 minutes. The cupcakes are done when a toothpick or small paring knife comes out mostly clean when quickly stuck in the cupcakes. These cupcakes are often done baking before they look done, and they will continue to bake a little bit as they cool. Because these cupcakes are so moist, it is okay to see a few moist crumbs on your knife when you check the finished product for doneness. But any wet-looking crumbs mean they need more time in the oven.
  • Brush Cupcakes with simple syrup (optional, see Note #2).
  • If you are frosting and serving them the next day, wrap the cupcakes in the cupcake tin and leave at room temperature overnight. You may also freeze the unfrosted cupcakes wrapped tightly in the cupcake tin up to a week in advance and they will stay very moist.

Decorate and Serve

  • Fill with your favorite Cupcake Filling and frost with your favorite Buttercream Frosting. I like to use 18" disposable pastry bags and either a 1M star tip or Round Cupcake Tip to pipe frosting on these cupcakes. Decorate with a drizzle of chocolate ganache using a squeeze bottle, if desired, and top with your desired garnishes.
  • Store finished cupcakes in airtight Tupperware. Cupcakes are best eaten at room temperature. If not serving within 24 hours, refrigerate the frosted cupcakes, but remove from the fridge 2-3 hours before serving so they may come back to room temperature. Enjoy!


  1. Read my article Instant Clearjel: a Magical Bakery Ingredient to see why I think this ingredient is worth having in your pantry.  Instant Clearjel must always be whisked thoroughly with other dry ingredients before added to wet ingredients to avoid clumping.  I have tested this recipe with the following Instant Clearjel brands: Prepared Pantry, Hoosier Hill Farm, and Ingredion (Make sure what you purchase is labeled as “Instant.”  Cooktyle Clearjel is a different product that does not work the same in cakes).  If you don’t have Instant Clearjel you can substitute Jello Chocolate Instant Pudding Mix as described in my Instant Clearjel Substitutes.  
  2. Simple Syrup is optional, but I highly recommend it to seal in the moisture of your cupcakes.  While the cupcakes cools, make a simple syrup by combining 2 tsb water and 2 tsp sugar in a small microwave-safe bowl. Microwave until the sugar is dissolved after whisking, about 20-30 seconds.  You can also make a larger batch of this (1 part sugar to 1 part water) and keep it in the fridge if you’re doing a lot of cake/cupcake baking.
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Course: Dessert
Cuisine: American
Keyword: bakery recipe, bakery-style cupcakes, chocolate cupcakes, cupcakes, moist chocoalte cupcakes
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mary powell
mary powell
4 months ago

5 stars
I’ve already enjoyed the Triple Chocolate Ganache, Chocolate cake with ganache and Vanilla buttercream. Can’t wait to make the chocolate cupcakes with Peanut Buttercream.

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