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Freshly Milled Vegan Chocolate Cupcakes

These easy vegan chocolate cupcakes with freshly milled flour are soft, rich and deeply chocolatey. They contain no applesauce, eggs or dairy and come together in just one bowl. No one ever guesses that these are made with whole grains! Either frosted or plain, they’re soft and decadent and everything a chocolate cupcake should be.
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Closeup of vegan chocolate cupcakes on a black cooling rack, frosted with chocolate ganache and colorful spring-themed sprinkles
5 from 1 vote
Prep Time:10 minutes
Cook Time:20 minutes
Cooling Time:15 minutes
Total Time:45 minutes
Servings:12 Cupcakes
Calories:170kcal
Equipment
Ingredients
  • 195 g fresh milled flour* - (see Notes to choose the right grain) 1½ cups
  • 200 g raw cane sugar* - (see Notes for adjustments) 1 cup
  • 3 tbsp cocoa powder - (dutch process, preferably sifted)
  • ¼ tsp fine salt
  • 1 tsp baking soda
  • 1 tsp vanilla extract
  • 1 tsp fresh lemon juice - (or apple cider vinegar/white vinegar)
  • 65 g coconut oil - (melted) ¼ cup + 1 tbsp
  • 240 g water* - (see Notes for adjusting to different grains) 1 cup
Instructions
  • Preheat oven to 175°C (350°F) and line a muffin tray with paper liners. Alternatively, grease the molds well with coconut oil.
  • Grind your whole grains on the finest setting of your grain mill.
  • Combine the dry ingredients in a large bowl and stir until everything is well combined. Make a well in the middle of the dry ingredients.
  • Add vanilla extract, lemon juice, coconut oil and water. Gently stir until just combined and no pockets of flour remain.
  • Divide the batter evenly between the molds of muffin tray. Bake for 20-25 minutes or until a tester inserted in the center comes out completely clean.
  • Rest the muffin tray on a cooling rack for 15 minutes before removing the cupcakes and letting them cool completely.
Notes
Grain Swaps (Adjust Water as Needed):
Spelt or Soft Wheat: Light and cakey, no changes needed.
Spelt + Kamut (1:1): Airy crumb with added structure—great base for frosting!
Hard + Soft Wheat (1:1): Added structure without ancient grains.
Einkorn: Reduce water to 225g (1 cup - 1 tbsp).
Kamut: Increase water to 255g (1 cup + 1 tbsp).
Whole Grain Wheat or Spelt flour (store-bought): Works without changes.
No matter the flour, aim for a loose, pourable batter.
Sugar: For a bakery style cupcake, keep the sugar as written. Personally, I find 3/4 cup more than sweet enough, especially if you plan to add frosting or ganache.
Mixing: Do your best to avoid over mixing the batter. Less mixing = softer cupcakes.
Cooling: Make sure to rest the cupcakes 15 minutes before removing from the muffin pan. They’ll be too tender right out the oven. It’s also key in making sure that the paper liners don’t stick after cooling.
Frosting: Let Cupcakes cool off completely before adding any frosting. Otherwise it could melt and slide right off.
Author: Sarah | Grains & Greens Kitchen
Calories: 170kcal
Tried this recipe?Let me know how it turned out!