13 Tips For Baking With Freshly Milled Flour, Including Sourdough

Milling flour at home using countertop stone mills has become increasingly popular in recent years, particularly alongside the rise of the sourdough bread trend. The lockdowns have played a role in both movements, and they are just growing in popularity from everything I’m seeing. I was newly pregnant with our first baby during the start of the chaos. This is before we bought our homestead and were living in a condo. It didn’t take long to start feeling the effects of cabin fever from being cooped up, so I decided to buy a grain mill and try my hand at making sourdough bread with freshly milled flour.

Working with fresh milled flour had a steep learning curve, but I’ve stuck with it and gotten pretty good at it.

Many recipes require sifting the flour to eliminate the bran or adding substances such as vital wheat gluten and soy lecithin. Home-milled flour, which contains the bran and germ, will significantly affect the texture and rise of baked goods. As a result, most recipes you come across might only use a small portion of home-milled flour, with the remainder being white bread flour.

Even commercial whole wheat and whole grain flours are challenging, but it is nothing compared to fresh milled.

I’m skeptical of recipes that claim you can easily swap out the store-bought flour for freshly milled and proceed as normal.

It’s mostly a lie. One example where it works is my easy fresh milled flour cookie recipe because of the way that particular cookie is made, but for a loaf of bread? No.

Mastering the craft is achievable by keeping key things in mind. But be warned — this might become a new obsession.

Let Go of The Notion That Freshly Milled Flour Will Ever be Similar to White Bread Flour

Photo Credit: The Peasant’s Daughter.

Freshly milled flour differs from white flour. If you’re used to seeing open, airy crumbs in white sourdough bread, you won’t get the same result with freshly milled flour. However, you also won’t be able to achieve the trendy, rustic crumb shots with whole grains and whole wheat flours from the store either.

And that’s okay. 

Your bread will taste delicious and have a rustic charm, regardless of any aesthetic imperfections. Our focus is on flavor, quality, and nutrition.

And yes, soft and chewy delicious crumbs that don’t fall apart are very achievable with freshly milled flours and ancient grains.

Freshly Milled Flour is Thirsty (Except for Spelt)

Photo Credit: Envato Elements.

I highly recommend you do this experiment every time you start baking with a new whole grain flour or freshly milled: mill 500 grams of the flour and divide it up into 5 bowls, 100 grams per bowl.

Add a different hydration percentage relative to the flour to each bowl, starting around 70% and working your way up in increments.

I do 75%, 80%, 85%, 90%, and 95%.

Every half hour I’ll check on the bowls (make sure they’re covered) and play with the dough to see how it feels, looks, and is behaving. Is it stretchy? Crumbly? Tearing?

You will learn much about the flour you’re using or milling and what it likes and can tolerate regarding hydration.

Use my simple sourdough calculator to calculate the hydration levels of the above experiment automatically and adjust your recipes for all your sourdough baking.

Higher hydration recipes and techniques will favor freshly milled flour, which has much higher absorption rates.

Because freshly milled flour absorbs more water, you must add more liquid than usual. Start by increasing the recipe’s water by 5-10% and adjust from there. Hydration can make or break your bread, literally. It’s all about finding that sweet spot where the dough is workable, and the bread is moist.

Spelt is an outlier here and does not prefer higher hydration levels.

Try Scalds & Tangzhong

Photo Credit: Envato Elements.

Incorporating scalds or Tangzhong (a technique borrowed from Japanese baking that involves cooking a portion of the flour and liquid in the recipe until it forms a paste) can dramatically improve the texture of bread made with freshly milled flour.

These methods gelatinize the starches in the flour, allowing them to absorb more water and retain it throughout baking. This results in a softer, more tender loaf with a better shelf life. Experiment with scalding some whole grains or using Tangzhong with your freshly milled flours to see how it changes the final product.

You can use milk or water depending on the desired result.

Try a Sponge

Photo Credit: The Peasant’s Daughter.

In bread baking, a sponge is a pre-fermentation mix of flour, water, and active sourdough starter yeast, sometimes with a little sugar. It ferments for hours or overnight, creating a bubbly texture. This process deepens the bread’s flavor, improves its texture, and can extend freshness. After fermenting, the sponge is added to the main dough, infusing it with these qualities.

This technique, used in recipes like sourdough and baguettes, enriches the bread’s taste and structure, making it a favorite for artisan baking.

Autolyse is Your Friend 

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An autolyse period, where the flour and water in your recipe are mixed and allowed to rest before adding sourdough starter (or commercial yeast) and salt, is particularly beneficial with freshly milled flour. This rest period hydrates the flour thoroughly, starts the gluten development process, and makes the dough easier to handle and shape.

It can also enhance flavor and texture, yielding a loaf with superior qualities. With freshly milled flour, consider extending the autolyse period to up to an hour or more to maximize these benefits.

Add Milk or Whey

Photo Credit: Envato Elements.

Incorporating milk or whey into your bread recipes can enrich the dough, providing additional sugars, fats, and proteins that can enhance browning, flavor, and texture.

Milk softens the crumb and crust, which can be particularly appealing when using freshly milled flour, which tends to produce heartier breads.

Whey, a byproduct of cheese and yogurt making, adds a subtle tang and tenderizes the gluten, making for a flavorful and tender crumb.

If your freshly milled loaves (especially those sandwich loaves) are falling apart or have a very crumbly and stiff crumb — add milk or whey.

Add Fat

Photo Credit: Envato Elements.

Adding fats like butter, lard, olive oil, or coconut oil can improve the mouthfeel and flavor of bread made with freshly milled flour.

Fats coat the flour particles, which can help to tenderize the crumb and soften the crust. This is especially useful when working with whole grain flours, as it can balance the density and add richness to the final loaf.

Adding fat to a loaf also increases the time required for bulk fermentation.


Photo Credit: Envato Elements.

Incorporating eggs into your dough adds moisture, fats, and leavening agents that can help to create a lighter, richer bread. The natural lecithin in egg yolks acts as an emulsifier, improving the dough’s structure and enhancing the bread’s shelf life.

Eggs can be particularly beneficial in recipes that might otherwise result in denser loaves due to the freshly milled flour.

Instead of ultra-processed soy and sunflower lecithins, why not add eggs instead?

Use Your Regular Sourdough Starter

A pan-loaf and round Greek tsoureki Easter bread.
Photo Credit: The Peasant’s Daughter.

Instead of rushing to create a new sourdough starter made entirely with freshly milled grains, keep using your regular one made with store-bought flours, even white or all-purpose flours. It’s not cheating and it’s not wrong.

Sourdough starter maintenance is pretty simple once you understand a few basic things, but switching to fresh milled is going to be challenging simply because the starter will peak quickly and then begin to deflate.

Common problems will include intense acidity leading to a gradual weakening of the starter if you don’t know what you’re doing.

So just hold off at the beginning and wait until you have a routine and rhythm you’re comfortable with.

On Sifting

Photo Credit: Envato Elements.

A very controversial topic in the freshly milled bread-baking world, believe me. People will get absolutely fired up about this every time it comes up.

But while sifting freshly milled flour might seem counterintuitive, it can be useful for achieving specific textures or when you’re blending flours.

Sifting can help aerate the flour, remove any larger bran or germ pieces that might cut through gluten strands, and make for a lighter loaf.

However, don’t discard what’s sifted out; consider adding it back to the dough later or using it in other recipes to ensure you’re benefiting from all the nutritional value your grains have to offer.

Don’t be afraid to experiment just because someone told you it was bad to sift. You’re not a starving 16th-century peasant; you’ll do fine with some bran removed. And besides, it’s nearly impossible to remove all of the bran when you’re sifitng at home.

Start With a Higher Percentage of White Bread Flour

Photo Credit: Envato Elements.

Instead of diving into a 100% freshly milled einkorn boule, why not start with 10% and gradually increase the amounts, taking careful notes of how the flour and bread responds?

Additives & Conditioners

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While the aim is to keep bread as natural as possible, sometimes a little help from additives like vital wheat gluten can make a significant difference, especially when baking with low-protein flours. These additives can improve the dough’s elasticity and the bread’s volume, making for a more satisfactory loaf without detracting from the health benefits of using freshly milled flour.

Grain Choice Matters

Photo Credit: Envato Elements.

Not all grains behave the same way when milled and baked. Experimenting with different grains can reveal a wide range of flavors, textures, and nutritional benefits. For example, ancient grains like einkorn or emmer offer unique tastes but can be more challenging to work with due to their gluten structure.

Starting with more forgiving grains such as hard red wheat or white can be a good introduction to baking with freshly milled flour.

Baking with freshly milled flour is a journey of discovery and a trip through history. Each loaf offers insights and lessons, bringing you closer to mastering this rewarding art.

The key is experimentation, patience, and a willingness to learn from each bake.

Diving Into Homemade Flour & Countertop Milling

Photo Credit: The Peasant’s Daughter.

Make sure you check out my article on freshly milled flour for beginners for more information on the why of freshly milled grains. I mean, what is the point even?

Read More: Milling Flour at Home: Everything a Beginner Needs to Know

Sourdough Tools

xPhoto Credit: The Peasant’s Daughter.

I designed a fun automatic calculator for the sourdough bread baker to help you scale recipes up and down, change recipes, and play with things like hydration levels.

See It In Action: Simple Sourdough Calculator

Ancient & Heritage Grains

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A growing collection of breads and things made with heritage and ancient grains. One of the joys of home milling is the world of grain possibilities you’re opening up.

Read More: Ancient & Heritage Grains Recipes

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