Chocolate Cupcakes with Freshly Milled Flour

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These chocolate cupcakes made with freshly milled flour and chocolate icing are anything but basic. Serve these up to your family and friends when you need a simple and delicious dessert. The chocolate cupcakes improve if they are refrigerated overnight due to the freshly milled flour, so it’s a great make-ahead dessert! If you make these with freshly milled whole einkorn, the cupcakes actually become more like a fudgy brownie after refrigeration!!

Chocolate cupcakes on a white plate with the title "Chocolate Cupcakes With Freshly Milled Flour."

For special occasions like birthdays and family get-togethers, I like to whip up these delicious chocolate cupcakes. You can tailor these cupcakes to whatever you have on hand and they are almost fool-proof!

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Making Chocolate Cupcakes With Freshly Milled Flour

This easy recipe will make 24 chocolate cupcakes. I will go over the ingredient substitutions you can make, but I wanted you to have my original recipe, too.

Tools:

Ingredients for Chocolate Cupcakes:

  • 2 sticks unsalted butter
  • 4 heaping tablespoons of cocoa powder
  • 1 cup very hot water
  • 2 cups flour
  • 2 cups sugar
  • 1/4 teaspoon salt
  • 1/2 cup plain yogurt
  • 1 teaspoon baking soda
  • 4 eggs
  • 2 tablespoons vanilla extract

Instructions for Baking Chocolate Cupcakes with Freshly Milled Flour

First, preheat your oven to 350°F (175°C).

Second, get out your grain mill and grind some flour. You’ll need 2 cups.

If you’re not into that or don’t have a grain mill, all-purpose flour works, too.

Grain mill with whole wheat berries.

If you have wheat berries or einkorn grain, grind them at the finest setting you can get. I haven’t ever noticed a baking quality difference in using soft or hard wheat, white or red wheat, so use what you have on hand.

Tip: For the most fudgy chocolate cupcakes after refrigerating overnight, use freshly milled einkorn flour! It’s magical!!

White bucket of freshly milled wheat flour.

Then get out the rest of the cupcake ingredients.

You’ll need cocoa powder, sugar, plain yogurt, fine sea salt, hot water, eggs, baking soda, unsalted butter, and vanilla extract.

Ingredients for making chocolate cupcakes sitting on a counter.

In a medium sauce pan over medium-low heat, melt 2 sticks of unsalted butter (8 ounces) and add 4 heaping tablespoons of cocoa powder. Whisk together well.

Next, add 1 cup of very hot water. Whisk everything well and let the mixture bubble on the stove for about 30 seconds. Then remove the sauce pan from the heat and allow it to cool down.

Medium sauce pan with melted butter and cocoa powder on a stove.

In a large mixing bowl, combine 2 cups of flour, 2 cups of sugar, and 1/4 teaspoon of fine sea salt.

As mentioned above, you can use all-purpose flour if you don’t use freshly milled flour.

Also, I like to use organic cane sugar because it has some molasses flavor and isn’t as highly processed as plain white table sugar. But use what you have on hand.

Pour the cooled chocolate mixture into the large mixing bowl with the flour and sugar and mix well.

Large glass bowl on a counter with flour and sugar inside and melted chocolate poured on top.

In a separate measuring cup (or mason jar with measuring lines), add 1/2 cup of plain yogurt, 4 eggs, 1 teaspoon of baking soda, and 2 tablespoons of vanilla extract. (I wrote a whole post if you want to make your own vanilla extract for cheap.)

Substitutions:

If you don’t have plain yogurt, you can also use buttermilk. Alternatively, you can use milk mixed with a tablespoon of lemon juice or white vinegar and let it set for about 5 minutes to clabber. You can also use any mixture of sour cream and milk.

Woman mixing ingredients to make chocolate cupcakes.

Pour the egg and yogurt mixture into the chocolate mixture and whisk together well.

If you have little helpers in the kitchen, mixing is a great job for them!!

Stir until the cupcake batter is smooth.

Little girls whisking ingredients to make chocolate cupcakes.

Line two muffin pans with parchment cupcake liners.

Scoop out some cupcake batter using your large cookie/ice cream scoop and fill each cupcake liner.

Two muffin pans lined with parchment paper with uncooked chocolate cupcake batter inside.

Bake at 350°F (175°C) for 16 to 18 minutes until a toothpick comes out clean. Be careful not to over-bake the cupcakes!

Two dozen chocolate cupcakes freshly baked in muffin pans sitting on top of a stove.

Cool completely before adding icing.

Instructions for Making Chocolate Icing

Ingredients for Chocolate Icing:

  • 22 oz powdered sugar
  • 4 heaping tablespoons of cocoa powder
  • 1/2 stick unsalted butter, softened
  • 2 tablespoons vanilla extract
  • milk
Ingredients for making chocolate icing sitting on a counter.

In a mixing bowl, combine powdered sugar and cocoa powder. Then add the softened butter and mix well.

Stand mixer with whisk attachment over bowl with sugar, cocoa powder, and softened butter.

Add a few tablespoons of milk until the sugar and cocoa powder start coming together.

Then add the vanilla extract and mix well.

Keep adding tablespoons of milk until the icing is smooth but firm.

Stand mixer with freshly made chocolate icing next to a bakery box of chocolate cupcakes made with freshly milled flour.

Get your cooled cupcakes out of the muffin pans. (I like to use disposable cupcake boxes when I need to take cupcakes on the go.)

Get out your icing piping bag and the star tip.

Tip: I wouldn’t use a plastic sandwich bag as a substitution for an icing piping bag. Speaking from personal experience, they pop and turn into a big mess!

Cut the tip off your icing piping bag and insert your decorating tip. Fold the top third of the bag down.

Woman holding an empty icing piping bag with star tip.

Use your spatula to scoop and press icing into the bag. Leave a few inches at the top of the icing bag, then twist the top of the bag closed and squeeze out some icing back into your bowl to get the air bubbles out.

Woman holding icing piping bag with star tip and the bag is filled with chocolate icing.

Decorate your cupcakes.

To ice the cupcakes, start on the outside perimeter and squeeze out icing in concentric circles until you reach the center. (You can get really fancy with icing your cupcakes. All the cute icing tips make different shapes.)

Woman piping chocolate icing onto chocolate cupcakes in bakery box.

Refill your piping bag as needed and finish icing the cupcakes. You can also add other decorations like sprinkles.

A dozen chocolate cupcakes with freshly milled flour in a brown bakery box.

Then enjoy your cupcakes!

Recipe Card for Chocolate Cupcakes

Chocolate cupcakes on a white plate.
Print Recipe
5 from 1 vote

Chocolate Cupcakes with Chocolate Icing

These chocolate cupcakes are anything but basic. When you need to whip up a special dessert, these rich, chocolate cupcakes hit the spot.
Prep Time10 minutes
Cook Time17 minutes
Cooling and Icing33 minutes
Total Time1 hour
Course: Dessert
Cuisine: American
Keyword: chocolate cupcakes
Servings: 24 cupcakes
Author: Rebekah

Equipment

  • medium sauce pan
  • mixing bowls
  • measuring cups
  • measuring spoons
  • muffin pans
  • whisk
  • large cookie/ice cream scoop
  • parchment muffin liners
  • mixer with whisk or beater attachment
  • spatula
  • icing piping bag and tip

Ingredients

Chocolate Cupcakes

  • 2 sticks unsalted butter
  • 4 tbsp cocoa powder
  • 1 cup very hot water
  • 2 cups flour
  • 2 cups sugar
  • 1/4 tsp salt
  • 1/2 cup plain yogurt
  • 1 tsp baking soda
  • 4 eggs
  • 2 tbsp vanilla extract

Chocolate Icing

  • 22 oz powdered sugar
  • 4 tbsp cocoa powder
  • 1/2 stick unsalted butter
  • 2 tbsp vanilla extract
  • milk

Instructions

Chocolate Cupcakes

  • Preheat your oven to 350°F (175°C). In a medium sauce pan over medium to low heat, melt 2 sticks of butter and whisk in 4 heaping tablespoons of cocoa powder. Then add 1 cup of very hot water, let it boil and bubble over medium heat for about 30 seconds while whisking and remove it from heat.
  • In a large mixing bowl, combine flour, sugar, and salt. Set aside.
  • In a large measuring cup, mix together buttermilk, eggs, baking soda, and vanilla extract. Set aside.
  • Pour the cooled chocolate mixture into the mixing bowl with the flour and sugar mixture. Stir until well-combined. Then whisk in the buttermilk mixture and stir until smooth.
  • Line the muffin pans and fill with cupcake dough.
  • Bake at 350°F (175°C) for 16 to 18 minutes until a toothpick comes out clean. Cool completely before adding icing.

Chocolate Icing

  • In a mixing bowl, combine powdered sugar and cocoa powder. Then add the butter and mix well. Add a few tablespoons of milk until the sugar and cocoa powder start coming together. Then add the vanilla extract and mix well. Keep adding tablespoons of milk until the icing is smooth but firm.
  • Cut the tip off your icing piping bag and insert your decorating tip. Fold the top third of the bag inside-out.
  • Use your spatula to scoop and press icing into the bag. Leave a few inches at the top of the icing bag, then twist the top of the bag and press out some icing to get the air bubbles out. Decorate your cupcakes and refill your piping bag, as needed.

Storing Your Chocolate Cupcakes With Freshly Milled Flour

If you make cupcakes a day in advance, store them in cupcake bakery boxes or other containers in your refrigerator. They would be fine if left out overnight but keeping them in the refrigerator will make the cake taste even better the next day! Especially if you use freshly milled einkorn flour!!

If you have any freshly milled flour left over, store it in the freezer so the flour won’t go rancid. Remember, your whole grains have natural oils that will go rancid once the grains our ground into flour unless you plan to use it within the next few days. In that case, you can store your freshly milled flour in the refrigerator.

Instructions to Bake Cakes Using This Recipe

If you would like to make two round cakes (or any other shape), follow the above recipe but bake the two cakes at 350°F (175°C) for 24 to 26 minutes until a toothpick comes out clean.

If you want to make a 9″ x 13″ cake, follow the above recipe but bake the cake at 350°F (175°C) for 39 to 41 minutes until a toothpick comes out clean.

For baking a sheet cake (13″ x 18″), follow the above recipe and bake the cake at 350°F (175°C) for 19 to 21 minutes until a toothpick comes out clean.

Tips to store bulk grains like wheat berries

I buy my whole grains in bulk from Azure Standard and keep them in food-grade buckets. They are very economically priced!

Just be sure to put any grains in the freezer for at least three days when you get them home. Freezing the grains ensures that any uninvited and microscopic passenger eggs (rare) are killed before you store them and use them.

Leave a comment.

I’m curious. What is your favorite type of flour to use when baking cakes or cupcakes? Leave a comment below and let me know.

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KitchenAid stand mixer

cupcake bakery box with window

stainless steel icing tips

disposable piping bags

parchment cupcake liners

grain mill

organic hard white wheat berries

organic einkorn grains

Redmond real salt

cupcake scoop set

butter dish with lid

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6 Comments

  1. 5 stars
    These were easily the best homemade cupcakes I’ve ever eaten! Only thing I would do next time is cut the amount of sugar down. Otherwise they were AMAZING. Thank you so much! Will be making these again.

      1. Soft white would work well. You can also substitute other flours in this recipe like hard white (or hard red wheat) and it won’t make a noticeable difference.

  2. These were such delicious, moist chocolate cupcakes!! I used FMF, soft white wheat and I used peppermint extract for the flavoring. Thank you for a great and simple recipe!