From gluten free to fresh milled sourdough … Here’s why…

Gluten sensitivity is on the rise. But what if the problem isn’t gluten itself, but how it’s processed? Fresh milled sourdough—a traditional bread made from whole grains ground right before baking—could be the solution. Thanks to a natural fermentation process that breaks down gluten, fresh milled sourdough is often easier to digest, offering a return to real, wholesome bread without the discomfort. In this post, we’ll explore why fresh milled sourdough might just be the answer for gluten-sensitive bread lovers.

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What’s the hype with fresh milled sourdough?

For years, I prided myself on perfecting “healthy bread.” I thought I’d unlocked the secrets to how bread was meant to be enjoyed. But despite my efforts, my body disagreed—I always struggled with bread. After years of chronic health issues, I knew I needed big changes, and a holistic practitioner finally gave me a suggestion: I should go gluten-free.

This revelation shocked me. How could my beloved, naturally fermented bread be causing my gut issues? I admit, I’d once dismissed the idea of gluten sensitivity. As a believer, I couldn’t get past this thought that wheat was an ancient food, dating back to biblical times, it should be healthy right?

And the answer is, wheat is healthy. Wheat contains 40/44 essential nutrients needed by the body for survival. So you’re telling me that wheat is healthy, but bread is not? I couldn’t make it make sense.

Is gluten-free the answer?

I did end up going gluten-free for a while, which I feel was necessary to control my inflammation, but that’s a story for another day. When I was ready to reintroduce gluten, I resisted the idea that “people just shouldn’t eat bread,” as some in the paleo and other grain-free communities say. There had to be a reason for the rise in gluten sensitivity.

After digging into the issue, which we will explore today, I decided to switch our family to fresh milled sourdough. This changed everything. When we made the switch, the difference was remarkable. To understand why, let’s explore the key differences between fresh milled sourdough, and traditional all-purpose flour.

What is fresh milled flour?

Fresh-milled flour is, by definition, a whole wheat flour, meaning it uses the entire wheat berry. Unlike commercial flour, it’s milled at home right before baking, ensuring it’s as fresh as possible. This approach is a great example of using food in its most natural form. Let’s take a closer look.

Let’s break down the wheat berry…

Wheat as a food source hasn’t changed much over thousands of years, but the way we grow and process it certainly has. I had never grown wheat myself and knew little about its journey from field to flour, and I’m guessing many others are in the same boat. So, let’s break it down.

The wheat berry, the seed of the wheat plant, has three main parts. Despite the name “berry,” it’s more like a kernel.

1. Bran: The bran is the wheat berry’s outer layer, rich in vitamins and minerals—around 80% of the berry’s nutrients are here. It also contains insoluble fiber, which helps us digest the inner parts of the berry, especially the endosperm (we’ll get to that). But in store-bought flour, the bran is sifted and removed to create a softer texture and a longer shelf life. This was a lightbulb moment for me!
2. Germ: The germ is the smallest part of the wheat berry, packed with B vitamins, vitamin E, healthy fats, and minerals. It’s the part that would sprout into a new plant and is a primary source of wheat’s oils. This component is essential to creating a balanced, nutrient-dense food. When combined with natural fermentation in bread-making, it’ a powerhouse for gut health.
3. Endosperm: The endosperm makes up most of the wheat berry and is mainly carbohydrates and protein. This starchy component is what’s milled into white flour, which is nearly all starch (or gluten). Removing the bran and germ creates the lighter, longer-lasting flour on store shelves, but it loses much of wheat’s original nutrition and diversity as a food source.

You’ve probably seen “enriched” on flour labels. That’s because, since the 1940s, manufacturers have been adding back nutrients like iron and B vitamins to compensate for those removed during processing. In whole wheat, these nutrients naturally occur as part of a complete, digestible food, but commercial flour needs this artificial enrichment to make up for what’s lost.

Why choose fresh milled sourdough?

Number 1:

Freshly milled whole wheat flour is a complete, nutrient-dense food. When you grind the entire wheat berry at home, you retain all its natural nutrients, eliminating the need for artificial enrichment. This is one of the main reasons we started grinding our own flour.

Number 2:

The second reason is freshness. Even when you buy “whole wheat” options from the store, much of the nutrients are already lost due to age. Nutrients start to degrade as soon as the wheat berry is milled and the outer shell is broken. While sources vary on exact numbers, it’s widely believed that 40-45% of nutrients are lost within 24 hours of milling, and up to 95% within 3 days.

Our modern food system prioritizes shelf life over nutrient content. Most of what we buy at the grocery store has been processed for longer storage, which can mean weeks, months, or even years since harvest. For example, produce is coated, milk is pasteurized, flour is sifted, and preservatives are added—all to extend shelf life, but often at the expense of nutrients and ultimately, our health. This emphasis on longevity over nutrition contributes to widespread chronic health issues.

Number 3:

Another benefit of freshly milled flour is the storage life of wheat berries. Wheat berries can be stored for many years without losing nutrients, unlike store-bought flour, which typically has a shelf life of up to a year. Plus, wheat berries, in their whole form, aren’t prone to pests—a design feature that helps with self-sufficiency and long-term food storage.

Number 4:

Lastly, cost is a huge perk. Organic wheat berries are very affordable, especially when bought in bulk, making them a more economical choice than small bags of all-purpose flour from the store.

Choosing a Grain Mill

My experience in this area is somewhat limited, there are endless grain mills on the market and I have only tried a few. I do have a grain mill that I love and use daily in my kitchen—the Nutrimill Harvest. It’s a real workhorse! I highly recommend it.

Investing in a grain mill will be the biggest upfront cost when starting with fresh-milled flour. However, whole wheat berries are much more affordable than pre-ground flour, especially when bought in bulk (which I’ll cover next).

Nutrimill also offers a newer, budget-friendly model for those looking for a lower-cost option. Their impact grain mill that they recently launched is very cost effective. They have offered all of our readers additional savings with the coupon “acresandaprons” that you can use at checkout.

Sourcing your wheat berries

We source our wheat berries in bulk, from Azure Standard. We love their quality and buy many of their product in our home. They offer free local pick ups once a month. Check here to see if they have a drop near you. They also offer convenient shipping, but to cut costs we opt for their free pick ups, once per month.

Storing Your Wheat Berries

Whole wheat berries are easy to store long-term, but it’s best to keep them in a cool, dry place and protect them from pests or contaminants, especially if storing them for extended periods. I use food-grade buckets for this purpose.

We order 5-gallon food-grade buckets from Azure Standard and keep them in our basement. To further protect against pests, moisture, and contaminants, I store the buckets raised off the ground. We don’t store pre-ground flour because of its short shelf life and rapid nutrient loss after milling.

You can also store bulk items in glass mason jars for easy access and long-term freshness. I order half-gallon jars from Azure Standard, then use my ForJars vacuum sealer to create an airtight seal, keeping pests out and extending shelf life..

What type of wheat berries should you use?

This can be a complex topic, so let’s keep it simple. The two main types of wheat berries used in recipes are hard wheat and soft wheat.

Hard wheat typically has 11-15% protein, which contributes to a higher gluten content. The higher gluten provides elasticity and strength, helping bread rise and creating a chewy, airy texture. This makes hard wheat ideal for bread, rolls, and pizza dough. Hard wheat can be either hard red wheat (often with a robust, nutty flavor) or hard white wheat (with a milder flavor). If you’re gluten-sensitive, soft wheat might be a better option, though it has less gluten, which makes it challenging for bread-making.

Soft Wheat generally has 7-10% protein, resulting in less gluten. The lower gluten content makes soft wheat ideal for tender, crumbly baked goods like cakes, cookies, pastries, and muffins, as it produces a lighter, softer texture. Soft wheat is usually available as soft red wheat or soft white wheat, both of which are mild in flavor.

In short, I mostly use hard white wheat for sourdough, breads, and rolls. For pastries and sweeter baked goods—like cookies, cinnamon rolls, and muffins—I prefer soft white wheat for its lower protein and softer texture. I rarely bake with any red wheats at all.

Spelt is an ancient grain dating back to Biblical times. It has a higher protein content and does contain gluten, though much less than modern hybridized wheat. I don’t use spelt often, but it works well in cookies, muffins, biscuits, and quick breads. Some people with gluten sensitivities (though not celiac) can tolerate small amounts of spelt.

How much flour does one cup of wheat berries make?

I generally get about 1 and 1/4 cup flour from 1 cup wheat berries. I don’t sift my flour. I want all the goodness in there. I grind it, measure, and go. That being said, I almost exclusively measure by weight, as I find it to b

My best tips for baking with fresh milled flour

So, you’ve made the switch, got your grain mill and your wheat berries—now what? Can you use all your usual recipes? In short, no, but let me explain.

Fresh-milled flour and all-purpose flour are quite different, and most recipes won’t convert exactly. Below, I’ll share my best tips for adapting traditional sourdough recipes to fresh-milled flour. I also have a fresh-milled sourdough boule recipe here and a delicious focaccia recipe here if you’re looking for a starting point. Let’s dive in!

1. Adjust the Liquid: Fresh-milled flour absorbs more liquid than all-purpose or bread flour. When I first started, my dough turned out so dense I couldn’t even make an indent! Increasing the liquid by about 5-10% usually does the trick, but it may take some experimenting.
2. Trust the Dough’s Feel and Look, Not the Measurements: Fresh-milled flour behaves differently, so start with extra liquid and add more only if needed. Mix until the dough is sticky or tacky to the touch, then let it sit to fully absorb the moisture.
3. Cool Your Fresh-Milled Flour for Pastries: Freshly milled flour is warm, which is great for yeast breads but not for pastries that require cold butter. For flaky pastries, you want the butter to melt in the oven, not in the mixing process. When I need cool flour, I refrigerate or freeze it briefly after milling.
4. Skip the Extra Flour When Kneading: One of my early mistakes was adding too much flour while kneading, trying to get the soft feel of store-bought flour. Instead, use a small amount of oil (olive, coconut, or avocado) on your counter and hands to prevent sticking. If you’re using a stand mixer, there’s no need to add oil.
5. Avoid Over-Working your dough: Fresh-milled flour requires gentler kneading. My rule: allow for a few moments of rest time, even if the recipe doesn’t call for it. If your dough is not incorporating well, allow for 15-20 minutes or rest time, and then come back to it. You’ll notice the dough becomes less sticky as it absorbs the liquid.
6. Troubleshooting Flat or Dense Bread: If your bread is rising poorly or falling flat, you might be over-kneading or stretching the dough, which can weaken the gluten. You can also try reducing the rise time by 15-20 minutes, as fresh-milled flour ferments quickly—your yeast may be exhausted by the time it’s ready for the oven.
7. Measure by weight: I find that weight is a far more accurate measure in general, but especially for fresh milled. So invest in a cheap kitchen scale, you won’t regret it.

How much flour does one cup of wheat berries make?

I generally get about 1 and 1/4 cup flour from 1 cup wheat berries. I don’t sift my flour. I want all the goodness in there. I grind it, measure, and go.

With these tips, you’ll be able to adjust and get the most out of your fresh-milled flour. Happy baking!