The Ultimate Guide to Baking with Fresh Milled Flour

What is Fresh Milled Flour?

So what exactly is fresh milled flour? Simply put, it’s flour that’s been ground straight from whole grains like wheat, spelt, or rye right before you bake.

If you haven’t tried baking with fresh milled flour yet, let me tell you—you’re in for an incredible treat!

Fresh milled flour takes home baking to a new level, bringing a wholesome, nutty flavor and peak nutrition to all of your baked goods.

It’s a world apart from the typical store-bought stuff, and once you experience the difference and learn a few tips, tricks, and techniques for success, there’s no going back.

Fresh Milled Vs. Store Bought Flour

Unlike the flour sitting on grocery store shelves—which can be months (even years) old, fresh milled flour contains all the natural oils, fiber, and nutrients the grain originally had.

Fresh milled flour contains 40 out of the 44 essential nutrients needed for our health, compared to white flour which has 20 out of 44 essential nutrients, with an additional 5 nutrients added synthetically. Bagged whole wheat flour may have more than 20 nutrients, but it’s still not equivalent to fresh milled flour. Let’s look at why:

Flour that is going to be processed and packaged to sell at the store, even flour labelled whole wheat, has to go through a process that extends the shelf life of the product.

Flour Processing

In large-scale milling, the grain is separated into its three components: the bran (outer layer), germ (nutrient-rich core), and endosperm (starchy part used in white flour).

Wheat is processed in large batches. After wheat is milled and sifted, factories will process the individual components (bran, germ, endosperm) of the grain. However, the process strips away some nutrients and flavors. It has to–after all, they need to make bagged flour as shelf-stable as possible and some of these nutrients are prone to oxidation.

The removal and treatment of these individual components is to prevent flour from going rancid too soon. Unfortunately, some of the most nutritious components are what are prone to oxidation, such as many vitamins (particularly vitamin E), minerals, and healthy fats, so they are removed or treated to become shelf stable.

After processing, all components will get added back together at a certain percentage to meet the requirement to be called “Whole Wheat Flour.” This isn’t necessarily the exact percentage that the grains were to begin with, so it can vary from what you would naturally mill.

But it also means that the reconstituted product is slightly less nutritious than freshly milled whole wheat flour since many of the nutritious components of the wheat berry are also what are prone to going rancid.

That said, please don’t take this as me catastrophizing store-bought flour. I don’t believe in making perfect the enemy of good, and demonizing foods almost always backfires, especially for certain personalities or those prone to disordered eating.

We can focus on the wonderful properties of nutritious, whole foods like home milled flour without overdramatizing the negatives of alternatives. This is largely my philosophy as an NASM-certified nutrition coach.

Pros of Fresh Milled Flour

Now lets look at the pros of milling your own flour:

Nutrition

When you mill your own wheat berries, nothing gets stripped away in the refining process. You get the whole grain, in its purest, most flavorful form.

Why does that matter? The benefits are huge!

Not only does fresh milled flour offer a richer, nuttier flavor than older bagged flour, but it’s packed with more nutrition.

Store-bought packaged flour goes through heavy processing that strips out many of the vitamins and minerals contained in the wheat. With the less harsh home processing of fresh flour, most of the vitamins and minerals are still there, giving your family food that is nourishing and delicious.

See the above “Fresh Milled vs. Store Bought Flour” for more information.

Taste

Nothing beats the taste of fresh milled flour! It is nutty, wholesome, rich, and delicious.

As with any sort of new food, you may need to expose yourself to it a few times to appreciate the taste. There is a noticeable taste difference between fresh and packaged flour. Fresh flour is nuttier and earthy.

After you have had it a few times, I guarantee you will prefer it. Sometimes I buy a bag of whole wheat flour for recipe testing to see if my recipes can work with both fresh milled and whole wheat flour. While my recipes do typically work with both, I notice a distinct taste difference and do not enjoy bagged whole wheat flour anymore.

I compare it to grinding your own coffee beans–sure, preground coffee will do. But nothing beats the freshness of grinding your own right before you brew it.

More Stable Blood Sugar

One *possible benefit of baked goods made with fresh milled flour, especially if they don’t contain added sugar, are the minimized spikes to your glucose levels.

If you are not diabetic, this may not be of major concern to you. However, if you do have diabetes or known blood sugar regulation dysfunction, this is huge!

My husband is a type-1 (insulin dependent) diabetic and he wears a CGM (continuous glucose monitor). We notice a distinct and obvious difference between bread products made with fresh-milled flour vs white flour. White bread causes a spike for him and fresh milled whole wheat doesn’t at all. It really goes to show that not all carbs are created equal!

Of course, your results may vary. Everyone is different, and some people will react more to wheat than others. Some diabetics still deal with glucose spikes even with fresh-milled flour. But this is not worth glossing over if you’re a bread lover needing to improve your metabolic health.

Better for Your Microbiome

People are recognizing the importance of good gut health more and more these days.

First of all, whole grain products offer prebiotic fibers that white flours do not. This is indisputable.

Second of all, freshly milled flour is not treated with bleach or other preservatives that harm your gut microbes the way store-bought flour is. As discussed earlier in this article, the treatment is necessary to make a shelf-stable product.

This doesn’t mean that store-bought flour is useless or unhealthy, but it is worth considering, especially if you have some digestive issues that you’re trying to troubleshoot.

Cons of Fresh Milled Flour

I want to acknowledge that not everyone can mill their own flour for a number of reasons.

Cost

Grain mills aren’t cheap, and they do take up space that you may feel you don’t have. Outside of the mill itself, gone are the days where wheat berries could be found cheaper than flour. That used to be the case several years ago, but now wheat berries are priced more like a specialty food product.

Once you have a system down and a stockpile of grain, milling flour doesn’t have to take much time, but I’m not going to act like it is faster than buying a bag of flour at the store. We all know it’s not!

The Learning Curve

I’m not going to say baking with fresh-milled flour is as easy as that bag of all-purpose flour in your pantry. It’s not. All of our modern-day recipes were developed with bagged flour in mind, and baking with fresh flour requires a few techniques and considerations that aren’t written into most recipes anymore.

Let’s not make perfect the enemy of good. If the only way you can eat whole grain is to buy packaged whole wheat flour, that’s still better than highly refined bleached white flour and is a worthy step to take.

That said, I still believe milling your own flour is worth it if you have the means.

You can see in the photo above a pretty flat loaf of sourdough sitting on the back of the counter. This picture is from a couple of years ago when I was first experimenting with fresh milled flour in my loaves. It took me quite awhile to figure out how to get a good rise!

If you want tips for that, too, check out my guide for how to get an open crumb in whole wheat sourdough.

Supplies Needed to Mill Flour

Milling your own flour requires:

1. Grains
2. A way to grind them
3. Storage

I will get more in the grains piece in the next couple of sections. For now, let’s focus on how to grind them. (Note: links below are affiliate links. Affiliate links support my ability to make free content without costing you anything extra to purchase. I only ever link to items I trust and believe in).

Grain Mill Options

Electric home grain mills (such as Mockmill, Komo, Nutrimill, Wondermill, etc) are the easiest and most convenient way to grind your own grains into flour. That said, they aren’t necessarily cheap.

Most people just starting out aren’t sure if they want to invest much money into this hobby yet. Some other options include mixer attachments (such as the Kitchenaid attachment) and hand crank mills (like this Wondermill Hand Mill).

I used the Kitchenaid attachment for 8 months to get started before upgrading to a Mockmill 200. It’s fine if your mixer has a large enough motor (do not try to use it on a lower Kitchenaid model) and you have patience (it mills slowly). For best results, mill the grain/flour twice: first time, run the wheat berries through on a coarse setting. Then put the flour through a second time on the finest setting. This will not only mill significantly faster, but it will be easier on your mixer’s motor than trying to mill on the finest setting right away. I think the final texture is better, too!

That said, the mixer attachment still isn’t cheap and it’s price takes you half way to a reasonably decent electric mill. You’ll have to decide if it makes sense for you or not. Same with the hand crank mills.

How to Mill Grains without a Mill

Perhaps you can’t invest in another kitchen appliance right now or you just want to give it a try before buying anything.

You can use a blender, food processor, or coffee grinder. Keep in mind that your final product will not be as fine as it would be with a mill, and be careful not to overheat these appliances.

I would not expect these appliances to hold up well over time with frequent flour making, but you could certainly use them to trial baking with fresh flour before committing to another purchase.

Storing Grains

Whole, unmilled grains can be stored in airtight containers in a cool, dark, and dry area. Many people like to use large food-grade buckets with airtight lids. It is important to keep your grains covered so pests don’t get inside.

I like to keep smaller quantities easily accessible in large canisters in one of my kitchen cupboards (see photo below). The rest is stored in large bins in my pantry.

Once the grain is milled, the best thing to do is to use it immediately, however, if you’d like to mill a larger batch of flour at once, then you can put the flour in an airtight container in the refrigerator for up to a week, or store in the freezer for up to 6 months.

I just keep extra flour in the freezer because there is no downside – it doesn’t freeze solid, so you can use it right out of the freezer, and then you don’t need to keep track of how long ago you milled it.

Choosing Your Grains

Red wheat, white wheat, spelt, einkorn, rye, kamut…so many grains, so little time.

This is a topic we can certainly get in the weeds with, but for the purpose of this guide, I will share some generalities.

Hard wheat = higher protein, higher gluten-making potential. This is great for bread or anything that you would leaven with yeast (sourdough breads, too!) Hard wheats include hard red, hard white, kamut, spelt, and durum. (Note: not all of these “hard” grains make bread that mimics the texture most people are after, but again, that’s another topic for another day).

Soft wheat = lower protein, fluffy, soft, less gluten-forming potential. Not great for breads, but wonderful for muffins, cookies, etc. Anything you would use baking powder or baking soda to make. Soft white, einkorn, rye, barley, oats, etc.

Soft grains and hard grains can be mixed at varying percentages to achieve the flavor and textures you are after, too.

What is the Best Grain to Start With?

In my humble opinion, the best starting grain is hard white wheat. It is very versatile. It’s great for bread, but still makes awesome muffins, cookies, etc. You can use it for almost anything.

Note: Hard white wheat is still whole grain! It’s called hard white because the kernel is lighter in color than hard red.

Best Recipes for Fresh Milled Flour

If you’re ready to dive in, check out some of my favorite recipes featuring fresh milled flour in my Whole Grain Baking and Baked Goods Sections.

Some of my favorites are the following:

• Red Wheat Sourdough
• Banana Carrot Muffins
• Pumpkin Spice English Muffins
• Fresh Milled Sandwich Bread (Yeast)
• Sourdough Bierocks
• Dark Chocolate Macadamia Nut Cookies
• Sourdough Cherry Knots
• Sourdough Garlic Pesto Knots

Where to Source Wheat Berries & Other Grains

My favorite place to get wheat berries is bulk food stores, especially stores run by Amish or Mennonite communities. They have the best prices. Here is a post with a list of Amish bulk stores by state, however, it’s not all-encompassing (I can see they are missing one from my state, for example). Be sure to ask around locally, too! Farm Direct Facebook Groups are a good place to ask.

Next, consider Azure Standard. If you can’t get to a local bulk foods store, Azure Standard is almost certain to have the best prices after that. However, shipping can be extremely expensive unless you live near a drop spot location, in which case, it’s free. Check out this section of the Azure website to learn more about how their shipping works.

If Amish bulk stores or Azure don’t work for you, the next best thing is to start checking out independent retailers and comparing the prices after shipping is calculated. Shipping is rarely free for grains (or if it is, the grains cost WAY more–nothing is ever truly free, we are all paying for it one way or another).

It is hard to get an apples-to-apples price comparison on a single product. For example, a 50-lb bag of hard white wheat may cost $50 on one website and $75 on another. You think you have found an obvious winner until you look at the shipping costs for those sites. The best thing to do is load your cart and go part way through the checkout on each site until shipping costs get calculated, then compare them.

Here are a list of some of the best grains retailers:

• Breadtopia (one of my favorites)
• Breadbeckers
• Country Life Natural Foods
• Central Milling

Tips & Tricks for Baking with Fresh Flour

Baking with fresh milled flour is different than using store bought. Once you get the hang of it, the results are well worth it. The texture, flavor, and nourishment freshly milled grains provide bring your baked goods to a whole new level. Here’s what you need to know to make the most of this flour transition:

Understanding Hydration

Fresh milled flour can handle more water than bagged flour. Actually, it has the uncanny ability of being able to handle more liquid while also seeming very mushy once you add the liquids. Many people mistakenly think it needs LESS water because of this.

This is because it takes time for the water to be properly absorbed and then for the gluten formation to start developing. This is why all of my recipes call for a resting period after mixing the ingredients. The only thing that helps this process is time–you can’t beat the moisture into the dough faster by kneading. Just let the flour fully hydrate, THEN start to knead.

The bran and germ in the flour are thirsty, so sometimes you might need to increase the liquid in your recipes. Not always, though–fresh milled flour also has more moisture than old, dried-out store flour, and it really depends on the individual recipe as to whether or not your flour will need more liquid or not.

Sometimes you may find your dough feels dry after the dough resting period. In that case, you can slowly add more water until you reach the right consistency.

On the other hand, perhaps your dough is handling the hydration of the recipe just fine. If the dough comes together nicely in a smooth ball and isn’t overly sticky or goopy after a resting period, it’s good! The recipe contained enough moisture as written, and adding more liquid would be counter-productive.

Don’t be afraid to experiment—your dough will let you know what it needs!

Dough Consistency

Dough made with fresh milled flour can have a different texture than you might be used to. It can be dense, especially compared to white flour.

When people are first starting to bake with it, they often use too much flour because they are worried about the mushiness when first mixed. That results in an overly dense final product.

Have patience and don’t overthink it when starting to bake with fresh flour. With enough practice, you’ll learn exactly what your doughs and batters should look like for best results.

Proofing Time Differences

Since fresh milled flour is more dense, your dough may rise a little slower than with store-bought flour. The weight of the natural oils and bran can slow the rate of the rise for yeast breads.

That said, my experience with fresh milled sourdough is that it actually ferments much faster even if you don’t see a dramatic rise like you’re used to with white flour. Fresh milled flour is more enzymatically active which can kick your fermentation speed up a notch.

Some people say the opposite, but that’s never been my experience. Your results may vary, but when I make white breads for friends and family side by side with a whole wheat loaf, the white loaf takes at least 50% longer to ferment than my fresh milled dough.

For more tips on making sourdough with fresh milled flour, check out my 100% whole wheat sourdough recipe.

How Do I Substitute Fresh Milled Flour?

Here is the process I use to substitute fresh milled flour into all of my favorite recipes:

1) Measure by weight. I estimate each cup to be 130 grams. If my favorite recipe calls for 2 1/2 cups of flour, I would do 130 x 2.5 = 325 grams. That is the weight of the wheat berries I would measure and then mill.

2) Let the dough rest. After mixing the wet and dry ingredients, let the dough rest so the flour has time to fully hydrate. This is especially important if you are making bread–for bread, let the dough rest before you knead. For cookies, cakes, muffins, etc. let the dough rest after mixing. I like to do at least 30 minutes in the refrigerator for these items.

3) As you work with the dough, fresh milled flour will be stickier than bagged flour, but it should still be soft, smooth, and workable–not mushy, and not overly dense. Start paying attention to the texture of your doughs and batters and compare them to how the final product turns out. This will help you monitor your baking for future recipes.

4) Let breads rise in a warm place.

5) Don’t over or under-bake. Take the internal temperature of your baked goods out of the oven. Make sure enriched breads are at least 190°F, lean breads (like artisan loaves) are at least 205°-209°F, muffins, quickbreads, and cakes are at least 200°F (or until a fork comes out clean). For cookies, aim for 180°F, however, you can usually tell by sight and a slight touch when cookies are done, so temping them is not necessary.

Fresh Milled Flour FAQs