These freshly milled carrot cake cupcakes are made with whole grain flour, giving them a rich, nutty flavor and tender crumb. Packed with grated carrots, warm spices, and a hint of vanilla, they’re naturally sweet and full of nutrients. Top them with tangy homemade cream cheese frosting for the perfect healthy-ish dessert recipe.

These freshly milled carrot cake cupcakes are made with whole grain flour, giving them a rich, nutty flavor and tender crumb. Packed with grated carrots, warm spices, and a hint of vanilla, they’re naturally sweet and full of nutrients. Top them with tangy homemade cream cheese frosting for the perfect healthy-ish dessert recipe.

An exciting new chapter
I’m so excited to get into the world of freshly milled grains. Previously, I didn’t know the difference between “whole wheat flour” bought at the store, versus freshly milled at home. Now I’ve learned that not only is whole grain much more nutritious than regular, all-purpose flour, but freshly milled grain ensures the freshest and most nutrient-dense version of the grain. After being milled, the freshly milled flour starts to loose its nutrient density almost immediately.
For the past few years I have been saving up for a grain mill, and was so excited once mine finally arrived.
We’ve noticed that the freshly milled bread products are much more filling, and sustain us longer than the all purpose versions. I feel more like I’ve eaten a complete meal as opposed to just a carbohydrate.
But cooking with freshly milled flour isn’t a super simple conversion. For starters, 1 cup of unmilled wheat berries does not equal 1 cup of freshly milled flour. Instead it equals about 1 1/4 cup.
Also, there are many different kinds of whole grain to buy, and they all act differently in bread products. There’s hard red or white wheat, which is ideal for bread making because of the higher gluten content. Then, there’s soft wheat, which is better for products like pancakes, muffins, and more.
So today I’m starting a series dedicated to freshly milled recipes. I’m converting many of the sourdough recipes that I already know and love to freshly milled flour, once I figure out the right grain ratios and type of grain to use.
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Are freshly milled cupcakes moist?
These carrot cake cupcakes are actually much more moist than their all purpose version because whole grains retain the germ, which is the part of the wheat kernel that contains healthy fats and oils.
With the shredded carrots, shredded coconut, and freshly milled grain, you get a moist, yet nutty, cupcake that is well complimented by the sweet cream cheese frosting.
Are freshly milled cupcakes healthy?
Freshly milled wheat, especially when used right after milling, contains nutrients that are stripped away during traditional processing of refined flours. Some nutrients you get with freshly milled grain are fiber, Vitamin B1, B3, B6, and B9, Vitamin E, Magnesium, Iron, Zinc, Phosphorus, Selenium, Protein, and healthy fats. Read more about the benefits of freshly milled grain here.
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More Dessert Recipes from the Homestead
Einkorn Brown Butter Chocolate Chip Cookies
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Tools Needed
Medium and large mixing bowl, or a stand up mixer

Freshly Milled Carrot Cake Cupcakes Ingredients
Makes 20 cupcakes
DRY INGREDIENTS
3 cups freshly milled flour*
1 TB cinnamon
1 tsp each ginger, nutmeg, salt, and baking soda
*to get 3 cups freshly milled flour, scoop about 2 1/2 cups of wheat berries. I recommend soft white wheat for this recipe, but any wheat will do!
Where do you get wheat berries?
I bulk order wheat berries from Azure Standard. I like that they have high quality, organic wheat, and a wide variety of types to try. Use code Alexa10 and my referral link to give them a try!

WET INGREDIENTS & SUGAR
5 eggs
1 cup coconut sugar
3/4 cup maple syrup
1/2 cup coconut oil melted
8 tbsp (1 stick) butter, melted
1 TB vanilla extract
OTHER
3 cups shredded carrots (about 4 medium size carrots)
1 cup coconut flakes (optional)
Chopped almonds or walnuts (optional, for sprinkling on top)

FROSTING
1 1/2 packages of 8 oz cream cheese, room temp (about 12 ounces total)
4 tbsp (half a stick) butter at room temp
1 TB vanilla
1 cup powdered sugar
milk, 1 tablespoon at a time

A note on freshly milled flour variations
While you can use 100% freshly milled flour for this recipe, you can also change it up a bit. Feel free to use 50% all purpose flour, einkorn flour, or other flour of choice.

How to Make Freshly Milled Carrot Cake Cupcakes
Preheat an oven to 350 degrees and line cupcake trays with cupcake liners.
Add all the dry ingredients to a medium size bowl and stir to combine.
In a large mixing bowl or stand up mixer, add the wet ingredients and sugar. Mix on medium speed until well combined.

Slowly add the dry ingredients to the wet ingredients, about 1/3 at a time, and mix until well combined. Do not over mix.

Stir in the shredded carrots and coconut with a wooden spoon.

Use a ladle to scoop the cupcake batter into the prepared cupcake tins.
Bake the cupcakes for 25-30 minutes, or until a knife inserted in the center comes out clean.

Let the cupcakes cool completely before frosting.
To make the frosting, add the frosting ingredients to a large bowl or stand up mixer. Add just 1 tablespoon of milk to start and mix on medium until desired consistency is reached. You can add more milk if you need it to be creamier.

Top with chopped nuts, sprinkles, or just plain 🙂

FAQS:
What are the benefits of freshly milled flour?
Freshly milled flour means that you grind the whole grain wheat berries in a grain mill and immediately after that, you put them into a recipe.
For starters, whole grain flour is healthier for you because it retains the bran and the germ portion of the grain. Regular all purpose flour from the store is just the endosperm portion, which lacks many essential vitamins and nutrients.
After that, the freshly milling process ensures you have the highest amount of vitamins and nutrients from the whole grain. Just like an avocado or banana, when you open a fruit from it’s peel and expose it to oxygen, it starts to degrade. Wheat works the same way. This is why wheat berries can be stored for years but flour should not be.
So in summary, freshly milled flour has many nutritional benefits. Most notably is the higher fiber, protein, vitamins, minerals, and antioxidants.
Read more about the health benefits of whole grains here.
Can I substitute freshly milled flour in any recipe?
You can substitute freshly milled flour in any recipe, but you do want to make sure you’re using the correct wheat berry. For breads, you want to use a hard red or white wheat. For all other non-rising products, you can experiment with soft wheat or ancient grain.

Freshly Milled Carrot Cake Cupcakes
These freshly milled carrot cake cupcakes are made with whole grain flour, giving them a rich, nutty flavor and tender crumb. Packed with grated carrots, warm spices, and a hint of vanilla, they’re naturally sweet and full of nutrients. Top them with tangy homemade cream cheese frosting for the perfect healthy-ish dessert recipe.
Ingredients
DRY INGREDIENTS
- 3 cups freshly milled flour*
- 1 TB cinnamon
- 1 tsp ginger
- 1 tsp nutmeg
- 1 tsp salt
- 1 tsp baking soda
- *To get 3 cups freshly milled flour, scoop about 2 1/2 cups of wheat berries. I recommend soft white wheat for this recipe, but any wheat will do!
WHITE INGREDIENTS & SUGAR
- 5 eggs
- 1 cup coconut sugar
- 3/4 cup maple syrup
- 1/2 cup coconut oil, melted
- 1/2 cup butter, melted
- 1 TB vanilla extract
OTHER
- 3 cups shredded carrots (about 4 medium-sized carrots)
- 1 cup coconut flakes (optional)
- Chopped almonds or walnuts (optional, for sprinkling on top)
FROSTING
- 1 1/2 packages of 8 oz cream cheese, room temp (about 12 ounces total)
- 1/2 stick (4 tbsp) butter at room temp
- 1 TB vanilla
- 1 cup powdered sugar
- Milk, 1 TB at a time
A NOTE ON FRESHLY MILLED FLOUR VARIATIONS
- While you can use 100% freshly milled flour for this recipe, you can also change it up a bit. Feel free to use 50% all purpose flour, einkorn flour, or other flour of choice.
Instructions
- Preheat an oven to 350 degrees and line cupcake trays with cupcake liners.
- Add all the dry ingredients to a medium size bowl and stir to combine.
- In a large mixing bowl or stand up mixer, add the wet ingredients and sugar. Mix on medium speed until well combined.
- Slowly add the dry ingredients to the wet ingredients, about 1/3 at a time, and mix until well combined. Do not over mix.
- Stir in the shredded carrots and coconut with a wooden spoon.
- Use a ladle to scoop the cupcake batter into the prepared cupcake tins.
- Bake the cupcakes for 25-30 minutes, or until a knife inserted in the center comes out clean.
- Let the cupcakes cool completely before frosting.
- To make the frosting, add the frosting ingredients to a large bowl or stand up mixer. Add just 1 tablespoon of milk to start and mix on medium until desired consistency is reached. You can add more milk if you need it to be creamier.
- Top with chopped nuts, sprinkles, or just plain 🙂
Notes
Store up to 5 days in the fridge or freeze it for later.
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