How to Make Wholesome Einkorn Bran Muffins with Fresh-Milled Flour

Hi Sweet Friend! If you’ve ever wondered about the benefits of baking with freshly milled flour, I’ll show you how easy it is to make Whole Grain Einkorn Bran Muffins. You’ll enjoy this quick bread with all the benefits of fresh-milled flour in just about an hour.

Watch the Whole Grain Einkorn Bran Muffin Recipe video, where I walk you through every step of this recipe using fresh-milled Einkorn flour in my cozy kitchen. You can press play and bake right along with me! Be sure to also scroll down for helpful tips and the full printable recipe.

What is Einkorn?

Einkorn is one of the oldest forms of wheat known to humankind — often called an ancient grain because it has remained largely unchanged for thousands of years. Unlike modern hybridized wheat, Einkorn offers a gentle, wholesome flavor and a rich nutritional profile, making it a wonderful choice for traditional baking. Its name means “one grain” in German, referring to the simple way each seed is attached to the stem — a beautiful symbol of its pure and natural heritage.

Baking with Einkorn can feel a little different than baking with modern flours, but once you get the hang of it, it’s a joyful experience. Its soft, golden color and naturally sweet, slightly nutty flavor bring a special coziness to every recipe — especially these tender bran muffins!

Why Choose Einkorn Over Modern Wheat?

Einkorn is often easier for many people to digest than modern wheat varieties because it has a simpler gluten structure and a richer balance of protein, vitamins, and minerals. It’s naturally higher in lutein, antioxidants, and essential nutrients like zinc and iron—making it a wholesome addition to a traditional foods kitchen.

Choosing Einkorn connects us with the way our ancestors baked—using flours that nourished body and soul, free from modern modifications. When you bake with freshly milled Einkorn, you’re bringing a little bit of that old-world wisdom into your own home.

What is Fresh-Milled Flour?

Fresh-milled flour is made by grinding whole grains—like Einkorn, Spelt, or wheat berries—right in your own kitchen using a home grain mill.

How Is Fresh-Milled Flour Different From Store-Bought Flour?

Unlike store-bought all-purpose flour, which has often been sifted, aged, and stored for months, fresh-milled flour contains the entire grain: the bran, germ, and endosperm. And yes, store-bought whole wheat flour contains the bran and the germ, too, but like the all-purpose flour, it has been aged and stored for months, allowing for the nutrients contained in whole grain flour to degrade.

What Are The Benefits of Fresh-Milled Flour?

Fresh-milled flour is also full of flavor, nutrients, and natural oils that give baked goods a rich, wholesome taste and texture. It’s also more “alive,” which makes it behave a little differently in recipes—often requiring a bit more liquid and a gentle touch. But once you bake with it, there’s no going back. You’ll fall in love with the aroma, the taste, and the beautiful connection to the tradition of home milling.

Why Bake with Fresh-Milled Einkorn Flour

There’s something so comforting about baking with Einkorn—it’s the oldest wheat known to mankind, and when you mill it fresh in your own kitchen, you’re truly stepping into a timeless tradition.

I love how Einkorn brings a slightly sweet, nutty flavor to baked goods and how it feels so gentle on the hands when mixing. Because it has a different gluten structure than modern wheat, it doesn’t behave quite the same—and that’s part of the fun! It teaches you to slow down, to pay attention, and to bake with all your senses.

Whenever I use fresh-milled Einkorn flour, I feel like I’m not just baking—I’m nurturing my family with something deeply wholesome and full of history.

Why You’ll Love These Einkorn Bran Muffins

These are not your typical bran muffins—they’re better! Made with 100% whole grain Einkorn flour, sweetened gently with dark maple syrup, and loaded with raisins, these muffins are:

• Rich in fiber and nutrients
• Naturally sweet and moist
• Perfect for freezer-friendly meal prep
• An excellent introduction to baking with ancient grains

Plus, they’re a delicious way to start your day with something wholesome, comforting, and full of traditional goodness.

What Makes This Recipe Special: Fresh-Milled Einkorn Flour

If you’ve ever baked with store-bought flour and then tried fresh-milled flour, you know the difference is astounding. Fresh-milled Einkorn flour is more flavorful, more fragrant, and more nutritious—but it also behaves a little differently.

Here’s what you need to know:

1. It’s Thirsty Flour!

Freshly milled flour—especially Einkorn—absorbs more liquid. That’s because it still contains the germ and bran and hasn’t been sitting on a shelf, losing vitality. I’ve adjusted the liquid in this recipe to reflect this—so you’ll have a moist, tender muffin every time.

2. Gentle Handling Is Key

Einkorn has a more delicate gluten structure than modern wheat. That means you don’t need to overmix. Stir just until combined for the best texture.

3. You May Need to Let the Batter Rest

Sometimes, letting the batter sit for 5–10 minutes before scooping gives the flour time to fully hydrate. This waiting period is especially helpful when using fresh-milled flour with bran added in.

Ingredients for Einkorn Bran Muffins

Find the full printable recipe with ingredients below.

Find product links for equipment and ingredients, including ancient grains, below.

Dry Ingredients:

🌾 1 cup fresh-milled whole grain Einkorn flour

🌰 1/2 cup wheat bran

⚗️ 2 teaspoons baking powder

💨 1/2 teaspoon baking soda

🧂 1/2 teaspoon fine sea salt

🍂 1 teaspoon ground cinnamon

Wet Ingredients:

🥛 1 cup buttermilk (or whole milk with 1 tablespoon vinegar)

🍁 1/3 cup dark maple syrup (or honey if you prefer)

🧈 1/4 cup melted butter

🥚 2 large eggs

🍶 1 teaspoon vanilla extract

Mix-Ins:

🍇 1 cup raisins

🐿️ 1/2 cup chopped walnuts or pecans (optional, but if using, decrease raisins to 1/2 cup)

How to Make Einkorn Bran Muffins

Find the full printable recipe with instructions below.

Step 1: Preheat oven to 425°F (218°C). Line a muffin tin with paper liners.

Step 2: Mill your whole grain into flour. I use whole Einkorn berries and a countertop grain mill.

Step 3: Mix the dry ingredients. In a large bowl, whisk together the Einkorn flour, wheat bran, baking powder, baking soda, and salt.

Step 4: Add the raisins (and nuts if using) to the dry ingredients and toss to fully coat.

Step 5: In a separate bowl, whisk the eggs, buttermilk, maple syrup, melted butter, and vanilla extract.

Step 6: Add the wet ingredients to the dry ingredients and stir until just combined.

Step 7: Scoop the batter evenly into the muffin cups.

Step 8: Let the batter rest for 5 minutes.

Step 9: Bake at 425°F (218°C) for 5 minutes, then reduce the temperature to 350°F (177°C) and bake for an additional 15–18 minutes, or until a toothpick inserted comes out clean.

Step 10: Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.

Delicious Variations to Try

Swap the Raisins 🍇
Try chopped dates, dried figs, cranberries, or even diced dried apricots for a fun twist.

Sprinkle with Cinnamon Sugar 🍂
Before baking, lightly dust the muffin tops with cinnamon and a touch of raw sugar for a sweet, spiced finish.

Add Grated Apple or Carrot 🍎🥕
Stir in 1/2 cup of grated fruit or veg for extra moisture and a touch of natural sweetness—perfect for kids!

Boost the Spice 🌰🍂
Add 1/2 teaspoon ground allspice, nutmeg, or ground cloves to cozy things up.

Make Them Mini 🧁
Scoop the batter into mini muffin tins and reduce the bake time to about 10–12 minutes—great for lunchboxes or tea trays.

Best Tips When Baking With Einkorn

• Don’t overmix! As with all muffins and quick breads, a light hand is the key to success, but it is especially important when working with Einkorn.
• Don’t skip the rest period! This waiting period gives the bran time to soften and helps the muffins rise evenly.

Storing and Reheating Bran Muffins

Storing: Store your Einkorn Bran Muffins in an airtight container at room temperature for up to 2 days, or freeze them for up to 3 months.

Reheating: Allow frozen muffins to defrost, unwrapped, at room temperature. Enjoy as is, or place them in an oven set to 200°F (93°C) for approximately 10 minutes until warmed through.

FAQ: Your Einkorn Muffin Questions Answered

Learn More About Einkorn and Spelt

As you navigate this journey to learning how to bake with fresh-milled flour, be sure to watch my How to Make All Purpose Einkorn Flour at Home video, where I show you how to grind Einkorn berries into fresh-milled flour. (Note: What I share in this video can also apply to any whole grain when grinding.)

As a bonus, I also show you how to sift the grain to make different grades of flour, including an old-world all-purpose flour.

Once you have learned how to make your freshly milled, all-purpose flour, try my Spelt Pie Crust Recipe. This recipe is made with all-purpose Spelt flour and introduces you to another ancient grain you can bake with.

Yes, whole grain is nutritiously the best, but sometimes, having fresh-milled flour on hand that you have sifted into your own homemade all-purpose flour can be very handy—especially for making pie crusts and delicate baked goods!

Learn more:

• Wheat Berries FAQs – Frequently Asked Questions About Wheat Berries
• What is Kamut? And What Are We Supposed to Do with It?

Baking Tender Muffins with Fresh-Milled Einkorn Flour

Baking with fresh-milled Einkorn flour is a true joy—especially when you see how tender and nourishing your homemade muffins turn out! With its rich, buttery flavor and excellent nutritional benefits, Einkorn brings an old-world charm to every bite. Adding extra bran boosts the fiber and makes these muffins a hearty, wholesome treat your whole family will love.

Once you bake with freshly milled flour, you’ll never want to go back to store-bought! It’s a simple step that brings so much goodness right into your own cozy kitchen.

The Modern Pioneer Cookbook is Here!

The Modern Pioneer Cookbook is your roadmap as you begin or continue your Traditional Foods Journey. Make sure you have a copy of this bestseller on your kitchen bookshelf. It’s so much more than a cookbook—it’s a traditional foods manual!

Preorder the Modern Pioneer Pantry!

Ready to continue your Traditional Foods Journey? Then, be sure to preorder the second book in the Modern Pioneer Pantry Series—The Modern Pioneer Pantry. My upcoming book is your guide to learn how to preserve a variety of foods to stock your Four-Corners Pantry so that you’ll always have everything on hand to make nutritious homemade meals on a budget.

Grind Your Own Flour with the Mockmill

When it comes to electric grain mills, after I did A LOT of research, I decided to buy a Mockmill. And am I so happy I did! The Mockmill is a very affordable but beautifully crafted German-made mill that stone grinds grain with settings ranging from 1 to 10—fine to coarse ground grain.

Learn more about Mockmill electric grain mills for making fresh flour and their Flake Lover’s Flaker that flakes whole grain in minutes. (This is not a sponsored post, I bought the Mockmill products that I show you, and I’m a happy user of their devices in my kitchen.)

• Mockmill 100 Grain Mill unboxing
• Get the Mockmill 100 Stone Grain Mill (Same product I show you in my unboxing video.)
• Flake Lover’s Flaker from Mockmill in action (Using this device, you can flake whole grain in minutes.)

Alternatively, are you looking for a manual grain mill to help you create fresh-milled flour at home?

• Lehman’s offers a variety of manual grain mills and more for your traditional foods kitchen. (Use this link and promo code NEST15 for 15% off orders at Lehman’s.)

Stay in Touch with Mary’s Nest

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4. Order The Modern Pioneer Cookbook - Get a hardcover book of Mary's nourishing recipes from a Traditional Foods Kitchen. This bestselling cookbook is published by Penguin Random House with their DK imprint.
5. Preorder The Modern Pioneer Pantry - Be one of the first to get Mary's hardcover book about preserving food and making delicious meals from your Four Corners Pantry. Mary's second cookbook is also published by Penguin Random House.

I look forward to having you join me in my Texas Hill Country Kitchen!

Shop for items used in this blog post or video

Ingredients in This Video

• Maple Syrup – Organic
• Wheat Bran – Organic Unprocessed Coarse
• Einkorn Wheat Berries

Ancient Grain Wheat Berries

• Einkorn (Farro Piccolo)
• Emmer
• Spelt (Farro)

Whole Grain Flour

• Rye Whole Grain, Organic
• Hard Red Spring Wheat, Organic

Equipment in This Video

• Mockmill 100 Electric Grain Grinder
• Stackable Glass Bowl Set
• Large Measuring Cup
• Measuring Cups and Spoons
• Large Whisk
• Magic Whisk
• Spatula

Amazon Shop and Shopping Guide

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• Visit my Shopping Guide page
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Recommended Reading

• The Modern Pioneer Cookbook
• The Modern Pioneer Pantry
• Nourishing Traditions
• The Essential Home-Ground Flour Book
• The Fresh-Milled Flour Baking Book