This whole wheat chocolate cake recipe is super moist and delicious like the classic dessert! It’s loaded with all the decadent flavors of chocolate only healthier and more nutritious using grains! No one will even tell it’s made with freshly milled flour! Make the cake ahead and assemble it later!

whole wheat chocolate cake

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Our Sour Cream and German Chocolate Cake has just as moist and tender crumbs! Chocolate goes so well with fruits or raspberry sauce, throw in some fresh fruit between the cake layers for a yummy surprise!

Chocolate Cake With Whole Wheat Flour

Chocolate lovers rejoice! Rich chocolate cake with a delicious fudge frosting is perfect for a holiday or casual weekend gathering! This light and fluffy layer cake is a healthier take on the classic using freshly milled flour! Whole wheat flour is wholesome and it can taste just as good as the traditional chocolate cake!

whole wheat chocolate cake

This chocolate cake recipe was the perfect way to celebrate my boy! It’s literally, one of the best cakes to whip up requiring minimal decoration, yet yielding a super moist crumb! I love that it’s quick and easy and I can make the cake layers days in advance.

Best of all this cake has so much flavor, it’s light and fluffy and smothered with the most rich fudge buttercream frosting! Layers of chocolate cake couldn’t taste better!

freshly milled flour whole wheat chocolate cake

Tips For Making Healthier Chocolate Cake:

  • For the frosting, make powdered sugar by using organic cane sugar. Simply run it through a blender until it turns into powder.
  • Use the cream off of raw milk for richer frosting.
  • I buy soy-free semi-sweet chocolate chips from Azure Standard in case you have sensitivities.
  • Omit 1/2 cup oil and replace with 1/2 cup of sourdough starter. It can be active or a sourdough discard, this will make the cake easier to digest.
  • Use coconut oil to grease and flour the pans.
  • This cake is very versatile to suit your needs, make it dairy-free by using coconut or almond milk, a gluten-free flour mix, or healthy sweeteners of choice. There will likely be a substitute for most of the ingredients and the cocoa powder does a great job to cover up any imperfections.

whole wheat chocolate cake using freshly milled flour

Ingredients Needed:

The cake layers come together with simple pantry ingredients. I always make sure I have soft white wheat on hand for all of my baked goods! Make sure to weigh your whole grains first then use it all up for the recipe. This means you don’t have to measure it out in cups simply weigh the grains and that is how much you’ll need.

  • Cake Layers- are made from freshly milled soft white wheat, organic cane sugar, cocoa powder, baking soda, baking powder, salt, sunflower oil, buttermilk, eggs, vanilla, and coffee. I mix in the order given using my Kitchen-Aid stand mixer.
  • Fudge frosting comes together with butter, chocolate chips, cocoa powder, cream, powdered sugar, salt, and vanilla extract.

How To Make Whole Wheat Chocolate Cake:

It’s important to start with the right tools. I measure my grains with a scale for consistent results and use two 9-inch cake pans. You can use a hand mixer or whisk and mix everything in one bowl but I prefer to use my kitchen aid mixer. The fudge frosting couldn’t be easier to make as you melt all the ingredients in a saucepan and then cool to frost.

  1. Prepare the cake pans: grease and flour them. Preheat the oven to 350°F.
  2. Make the cake layers by mixing all of the cake batter ingredients in the order given (dry ingredients first then wet). Mix over low speed until all the flour is incorporated.
  3. Pour the chocolate batter evenly onto the prepared cake pans.
  4. Bake the cake layers at 350°F for 25-30 minutes.
  5. Cool for 10 minutes, then flip onto parchment paper until ready to use. This makes it easy to later flip the cake onto a cake stand as it won’t stick to the cooling rack. You can either frost it or wrap it with plastic wrap and freeze it for assembling later.
  6. Make the fudge frosting: combine all of the frosting ingredients in a small saucepan and bring to a simmer. You just want to melt the sugar. Pour into a 9×13 and slightly cool, then place plastic wrap over the top so the chocolate frosting doesn’t form a skin. Cool in the refrigerator for 30 minutes until the frosting thickens.
  7. Assemble and Frost the cake by placing one cake layer onto a serving plate smother with frosting and place the second layer over the top. I like to place my cake layers facing up so it’s not domed-shaped. Finish frosting the tops and sides.

How To Make Ahead and Store Whole Wheat Chocolate Cake:

The cake layers will store well at room temperature for up to 3 days or in the freezer if wrapped well with plastic wrap. Cool cake layers completely then double wrap with plastic wrap. Place onto a large tray and flash freeze then keep frozen for up to 2 months. Semi-frozen cake is easier to frost than tender cake layers. Once you frost the cake store it at room temperature in a cake dome for up to 3 days. Refrigerating the cake will make for a drier crumb and harder frosting always thaw at room temp before serving if keeping in the fridge.

how to store chocolate cake layers


Can I Use Store-Bought Whole Wheat Flour?

This sourdough bread recipe is specifically for freshly milled flour. Store-bought wheat flour is different than freshly milled flour and is usually made from hard wheat varieties like hard red or hard white. I use soft white wheat which is more of a pastry flour and perfect for cakes. However, you can make it with part all-purpose flour if using whole wheat flour from the store.

What Does Freshly Milled Flour Do for Cakes?

Milling fresh flour is like grinding fresh coffee, or spices, it has a much stronger, fresher, flavor and aroma. It will give you a very flavorful, really digestible, and highly nutritious baked good at the end.

The bran is packed with fiber and the wheat germ is full of vitamin B6, folate, thiamin, zinc, magnesium, manganese, and vitamin E. Depending on the type of grain I use (in cakes soft white wheat), it’s just as delicious and the best chocolate cake because you won’t miss out on the taste.


Tips for Making Chocolate Cake with Freshly Milled Flour:

  1. Freshly mill your own flour by using a grain mill and good quality whole grains. I use soft white wheat for most of my desserts like crepes, cookies, and cakes.
  2. You can make the cake batter with a wire whisking one bowl however, using a stand mixer is easier. I like to run it over low speed while I add the ingredients one by one in the order given. That way it’s mixing the batter effortless and pretty much hands-off.
  3. You can use hot or leftover cold coffee. I’ve tried both and it turns out either way. If I need coffee quickly I’ll usually make some from instant coffee granules.
  4. For easier prep frost the cake on semi-frozen cake layers. Since the cake layers are so tender and moist this rich fudge frosting can be a little heavier to spread.
  5. Invert cake layers on parchment for easier cleanup (wire racks can be a hassle to clean).
  6. Pour the hot fudge frosting into a stainless steel pan to cool. Glass pans tend to crack or break.

Whole Wheat Chocolate Cake Recipe

Prep Time: 20 minutes
Cook Time: 30 minutes
Total Time: 50 minutes
Servings: 8 slices
Author: Alyona Demyanchuk
This whole wheat chocolate cake recipe is super moist and delicious like the classic dessert! It's loaded with all the decadent flavors of chocolate only healthier and more nutritious using grains! No one will even tell it's made with freshly milled flour! Make the cake ahead and assemble it later!


  • 2 9-inch round cake pans



  • 2 3/4 cups freshly milled soft wheat  flour (310 grams of grain or milled flour)
  • 2 cups organic cane sugar
  • 1/2 cup cocoa powder
  • 1 1/2 tsp baking soda
  • 1 tsp baking powder
  • 1 tsp salt
  • 1 cup buttermilk
  • 2 eggs
  • 1 tsp vanilla extract
  • 3/4 cup hot coffee

Fudge Frosting:

  • 315 grams unsalted butter (that's 2 sticks plus 6 tablespoons)
  • 400 grams semi-sweet chocolate chips 
  • 1/3 cup cocoa powder
  • 1 1/3 cup heavy cream
  • 1 1/3 cup powdered sugar
  • 1/2 tsp salt
  • 1 tsp vanilla extract


  • chocolate cake prep
    Preheat oven to 350°F. Grease and flour two round 9-inch cake pans. Set aside.
  • making chocolate cake batter in a stand mixer
    Using a stand mixer with the wire whisk attachment, mix the cake ingredients in the order given, over low speed.
  • Pour the cake batter into the prepared pans and bake for 30-35 minutes or until a toothpick inserted comes out clean.
  • cooling cakes on parchment paper for easier clean up
    Cool cakes in the pan for 10 minutes then loosen the sides with a knife and gently invert over parchment paper. Cool completely.
  • To Make Frosting: melt together all of the fudge frosting ingredients in a small saucepan until smooth.
  • fudge frosting prep
    Pour it into a stainless steel 8x12 pan and cool for 15 minutes. Then cover the surface with plastic wrap and refrigerate until the fudge is set about 30 minutes).
  • Once the fudge frosting has thickened gather it all to the center with a rubber spatula for easier spreading.
  • Spread a tablespoon of frosting in the middle of the cake platter and top with one cake layer. This helps hold it in place. Top with frosting and repeat. Frost the cake and sides using a cake spatula. Refrigerate
  • whole wheat chocolate cake
    Store the cake in the refrigerator and allow it to thaw a few hours before serving for the frosting to soften.

Nutrition per serving

Serving: 1large sliceCalories: 1348kcalCarbohydrates: 120gProtein: 12gFat: 96gSaturated Fat: 45gPolyunsaturated Fat: 4gMonounsaturated Fat: 42gTrans Fat: 1gCholesterol: 177mgSodium: 714mgPotassium: 631mgFiber: 7gSugar: 91gVitamin A: 1701IUVitamin C: 0.2mgCalcium: 150mgIron: 5mg

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