Freshly Milled Vegan Chocolate Cupcakes (Whole Grain, One Bowl)

Soft, rich and deeply chocolatey—these freshly milled vegan chocolate cupcakes come together in just one bowl and no time. Made with pantry staples, no applesauce, and absolutely no weird substitutions, they’re your go-to fix when a chocolate craving strikes right now. Freshly milled flour adds a depth of flavor and nutrition—without compromising on texture like most whole wheat options. I swear, 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.

I take a bit of a purist approach when it comes to chocolate. I prefer a seriously dark chocolate, not overly sweet, with a good snap. By the same token, I have always preferred chocolate cake (and especially brownie) recipes that rely on cocoa powder instead of melted chocolate. I find that chocolate should stand on its own, just pure cocoa bliss, not weighed down by dairy and eggs. The result is a light and airy crumb and intense chocolate flavour!

Why You’ll Love This Recipe

One-Bowl Recipe: This recipe comes together in no time. Just whisk the dry ingredients, add the wet, stir it up—and boom, you’re done! No fancy equipment or complicated steps.

Ready in 30 minutes: The batter mixes up fast, even if you’re milling your own flour. You’ll likely be finished before your oven’s done preheating. I love using paper cupcake liners for even quicker prep and easy cleanup.

Healthy Chocolate Treat: Freshly milled flour makes these cupcakes feel like a wholesome choice—something you can hand over to small hands without a second thought. And if you need more convincing: cocoa powder is packed with antioxidants, magnesium, iron, and potassium, while coconut oil offers healthy fats. Proof that indulgence and nourishment can live in the same cupcake!

No weird stuff: If you’ve delved into the world of vegan baking, you’ll probably be used to raising an eyebrow over the ingredients list. These cupcakes are accidentally vegan, with classic ingredients. No applesauce, mashed banana and creamed coconut in sight. You’re welcome.

Ingredient Notes and Substitutions

Fresh Flour: I have tested these vegan chocolate cupcakes with Kamut, Einkorn, Spelt and European (soft) Wheat—freshly milled on the finest setting. If milling isn’t for you, feel free to use your favorite whole grain flour, or mix half all-purpose flour with half whole grain.

Sugar: I love the caramel notes of raw cane sugar, but coconut sugar, beet sugar or plain white sugar will work just as well. I keep the amount flexible, so you can always hit the right spot (more info here).

Cocoa Powder: I love using dark Dutch-process cocoa powder for an intense chocolate flavour. If you don’t have it, regular cocoa powder will work, just expect a slightly different taste and lighter color.

Lemon Juice: Baking soda needs another acidic ingredient to create bubbles, which helps the cupcakes rise and gives them an airy texture. You can swap it for white vinegar or apple cider vinegar. Don’t worry, the taste disappears during baking!

Coconut Oil: I prefer refined coconut oil because it’s neutral in flavor, but if you’re into the chocolate-coconut combo, you can use unrefined. If your coconut oil is solid, just pop the jar in the oven while it preheats (but please, don’t forget in there, remember it’s hot and don’t touch it with your hands!). You can also sub with avocado, mild olive, or any other healthy oil you like. Just steer clear of vegetable oil—your cupcakes deserve better.

Tools You May Need

Mixing Bowl: One large bowl is all you need for this one-bowl recipe! Bonus points if it has a pour spout.

Muffin Tray: Standard 12-cup size. No need to bust out anything special.

Paper Liners (Optional): For quick cleanup and mess-free cupcake removal. Also: cute!

Sifter (Optional): If your cocoa powder is clumpy or your inner perfectionist needs a moment.

Grain Mill (Optional): If you’re working with freshly milled flour. Not required, but oh-so-satisfying.

Digital Kitchen Scale (Not Really Optional): I weigh my flour. There is no other reliable way of measuring freshly milled flour and I don’t want you ruining a batch of chocolate cupcakes on my watch.

How to Make Freshly Milled Vegan Chocolate Cupcakes

01

Preheat the 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.

02

Combine the dry ingredients in a large bowl and whisk until everything is well combined (if you notice any stubborn clumps, sift them back into the mix). Make a well in the middle of the dry ingredients.

03

Add vanilla extract, lemon juice, coconut oil and water. Gently stir until just combined and no pockets of flour remain.

04

Fill the batter into the prepared muffin tray. Try to divide the batter equally.

05

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.

Tips

• For a bakery style cupcake, keep the amount of sugar as written. Personally, I find 150g (3/4 cup) more than sweet enough, especially if you plan to add frosting or ganache. It’s still sweet enough to make the cocoa powder sing but not enough to send you to the dentist. And lastly, if I plan to hand them to toddler hands, I scale it all the way back to 130g (2/3 cups), which is still enjoyable enough for adults, but it makes the whole grain character a lot more apparent.
• Do your best to avoid over mixing the batter. Less mixing = softer cupcakes.
• Make sure to rest the cupcakes 15 minutes before removing from the tray, so the cupcakes stay tender and the paper liners don’t stick after cooling.
• Wait until the cupcakes are completely cool before adding frosting—otherwise it could melt right off!

Grain Guide: Choosing the Right Freshly Milled Flour for Vegan Chocolate Cupcakes

If you haven’t baked with freshly milled flour yet, you’re in for a treat. Experiment with various grains and find the perfect flavor for your cupcakes!

When swapping grains, always watch the amount of water. It’s not complicated, just make sure the batter stays loose and pourable. If you’re new to fresh flour, I recommend starting with Spelt or Soft Wheat for a tender, light texture. Once you’re comfortable, feel free to experiment with other grains like Kamut or Einkorn:

I’ve also had great results with store-bought flours—whole wheat, whole spelt, and semi-dark spelt flour (German T 1050) all worked with no adjustments. I’d confidently say this recipe plays well with any mix of whole grain and all-purpose flour.

This flexibility makes the cupcakes a solid base for all kinds of seasonal or topped variations—but they also have my heart straight from the pan.

Variations

Double Chocolate: Add ⅓ to ½ cup dark mini chocolate chips for an extra indulgent cupcake. There’s something oddly satisfying about a melty chocolate chip in a still-warm cupcake. I’m especially fond though of the added snap after a night in the fridge.

Holiday Twist: If you’re in the market for a chocolate cupcake during the most wonderful time of the year, add 1 tsp each of cinnamon and pumpkin pie spice (or German Lebkuchengewürz) for a Christmas twist.

Chocolate and Orange: Grate the zest of half an orange and rub it into the sugar with your fingertips before mixing the batter. It’s a timeless, elegant pairing (and a nod to my favourite Danish chocolate bar: Appelsin krokant).

Espresso: Coffee deepens the chocolate flavor (and no, it won’t make them taste like coffee). Replace part of the water with a shot of espresso or add 1-2 tsp of instant espresso powder to the dry ingredients.

Frosting Friendly: These cupcakes are a great base for a generous swirl of your favorite frosting—peanut butter, classic vanilla, strawberry, or whatever fills your cup. Or do what I did: chocolate ganache and lots and lots of sprinkles! For a classic, coconut-free recipe (and everything you ever wanted to know about ganache), I recommend this article from Gretchen’s Vegan Bakery.

How to Store and Freeze

Fridge: Store your cupcakes in an airtight container for up to 3-4 days in the fridge or out. Let them come to room temperature for the best taste and texture.

Freezer: Freeze unfrosted cupcakes by wrapping them in plastic wrap and placing them in a freezer bag. They’ll stay fresh for up to 3 months. To thaw, just let them sit at room temperature for a few hours. If you want, add frosting after they’ve thawed.

Recipe FAQs

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Ready to bake these indulgent vegan chocolate cupcakes?
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