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 flour, the cupcakes actually become more like a fudgy brownie after refrigeration! Other fabulous desserts to make with freshly milled flour are double chocolate pecan brownies, easy fruit cake, German chocolate cake, and delicious banana bread.

For special occasions like birthdays and family get-togethers, I like to whip up these delicious chocolate cupcakes. They are almost fool-proof! You can also use the same recipe to make a sheet cake, double layer cake, or 9×13 size. I’ve added the extra information you’ll need down below and in the recipe card.

Why You’ll Love This Recipe

More nutritious – Freshly milled flour is a traditional “alive” food that retains all of the vitamins and nutrients that are naturally found in wheat berries (the grain used to make wheat flour). It’s a simple swap that you can make to secretly make your baked goods more nutritious. Your family will only know that your baked desserts taste better!

More flavor – Using fresh flour lets you customize recipes for the flavor you love. If you want a dark, nutty flavor, you can use hard red wheat berries ground into flour. If you want a lighter flavor and texture, use soft white wheat berries.

Moist baked goods – Your baked goods will be more moist and delicious if you use freshly milled flour versus anything else. Even pre-ground bags of whole wheat flour don’t compare with freshly milled flour.

Ingredients

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

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

You can swap out the yogurt with milk, buttermilk, sour cream, or any combination thereof. If using milk, use whole milk mixed with a tablespoon of freshly squeezed lemon juice and let it set for about 5 minutes so it will clabber.

You can also use any combination of freshly milled wheat flour that you like. Using all einkorn flour is delicious, but you can also use hard or soft wheat, and red or white wheat or any combination thereof. Most of the time I use an even mixture of hard red wheat and soft white wheat. If you don’t have a grain mill, you can use all purpose flour.

How to Make 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. I use a mixture of soft white wheat and hard red wheat.

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. It’s magical!!

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.

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.

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.

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 good vanilla extract.

I wrote a post on how to make your own vanilla extract for cheap if you’d like to learn!

Pour the egg and yogurt mixture into the chocolate mixture once it’s cooled enough, 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.

Then line muffin pans with parchment cupcake liners, scoop out some cupcake batter using an extra large scoop (about 1/3 cup), and fill each cupcake liner.

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

Cool completely before adding icing.

How to Make Chocolate Icing

This icing recipe is my go-to chocolate icing. It’s very rich, so be warned! You can also decrease the amount of sugar to suit your taste.

Ingredients

• 22 oz to 3 cups of powdered sugar – Sift it if there are large chunks of hardened sugar.
• 4 heaping tablespoons of cocoa powder – For best results, sift the cocoa powder if there are hard chunks.
• 1/2 stick unsalted butter, softened
• 1 tablespoon of good vanilla extract
• warm milk or heavy cream

In a mixing bowl, combine powdered sugar and cocoa powder. Then add the softened butter and mix with a wire whisk until it looks like coarse crumbles.

Add a few tablespoons of warm milk or heavy cream until the sugar and cocoa powder start coming together. Then add the milk or cream by tablespoons until it reaches the smooth consistency you like.

Then add the vanilla extract and mix well. Keep whisking on medium speed until the icing is smooth and fluffy.

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 your favorite tip. I usually use a 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.

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.

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.)

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

Then enjoy your cupcakes!

Tips

• If you make cupcakes a day in advance, store them in cupcake bakery boxes or an airtight container in your refrigerator. Keeping them in the refrigerator will make the cake taste even better and fudgier the next day!
• If you have freshly milled flour left over, store it in the refrigerator for short term use or the freezer for long term use so the flour won’t go rancid. Remember, your whole grains have natural oils that will go rancid once the grains are ground into flour.
• To store whole grains, I like to use food grade buckets with gamma seal lids along with oxygen absorbers. I buy my whole grains in bulk from Azure Standard. 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.

Recipe FAQs

More Desserts from the Farm

• Old Fashioned Chocolate Chip Cookies
• Chocolate Fudge: 100-Year-Old Family Recipe
• Low Sugar Carrot Pie Recipe
• How to Make Red Icing Without Red Food Coloring (or White, Blue, Pink, or Lavender)

If you try this recipe and love it, I would love if you gave it 5 stars! Also, tag me on Instagram @rivers.family.farm.