How to Bake Sourdough With Freshly Milled Flour | Easy Guide

ByEmily Rider Updated

Choosing to mill your own flour is a thoughtful step toward more intentional baking. It means you deeply care about what goes into your bread, how it’s made, and the flavor it brings to your baked goods.

This guide will walk you through how to bake sourdough with freshly milled flour—step by step—so you can bake loaves that are wholesome and flavorful.

And if you are wanting to make your own freshly milled flour sourdough starter learn how to make one here: How to Make A Freshly Milled Flour Sourdough Starter or want to learn how to make a regular sourdough starter read this guide: How to Make a Sourdough Starter | A Beginner’s Guide.

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Baking with freshly milled flour isn’t complicated once you understand how it behaves in sourdough. The flour is alive with natural enzymes and oils. It ferments differently, hydrates differently, and rewards you with loaves that are tender, rich, and deeply satisfying to make.

Inside this post, you’ll learn exactly what to adjust, how to work with the dough, and how to bake with confidence using your own freshly milled flour.

Not sure about a term or tool mentioned here?  Read this post, How to Mill Flour at Home | A Beginner’s Guide and Glossary Of Terms For Sourdough & Freshly Milled Flour, for quick reference and help.

A Cottage Milling Note

When I think back over my years with sourdough and freshly milled flour, I feel deeply grateful. I learned to shape loaves at my grandmother’s side as a little girl, and later, as a wife and mother, I found my own rhythm baking sourdough with freshly milled flour in our cottage kitchen.

Everything you’ll find here on The Modern Day Cottage comes straight from that lived experience.

Every recipe is tested exactly as written, every photo is taken in my own kitchen, and every guide reflects more than 25 years of hands-on milling and baking.

My hope is that what I’ve learned over decades of slow, real baking helps you skip the trial-and-error and find joy in the process sooner.

This blog has been a dream come true, and it’s an honor to pass along everything I’ve learned — so you can bring fresh flour, sourdough, and a slower rhythm of living into your own home with confidence.

Why You’ll Love This Guide

  • Cozy, cottage-worthy loaves – Freshly milled flour gives bread a warm, rustic depth that store flour can’t match. You’ll learn how to bring that old-fashioned character right into your own modern kitchen.
  • Grain-to-table connection – I’ll show you how milling your own flour ties every loaf directly to the grain in your jar, so your bread isn’t just homemade, it’s home-grown in spirit.
    Answers the “why is this fermenting so fast?” question. Fresh flour is alive with natural enzymes and nutrients, which means sourdough behaves differently. This guide helps you understand the “why” behind it all, so you can adjust your starter and dough with confidence.
  • Hydration made simple – Freshly milled flour absorbs more water than store flour. You’ll learn exactly how to balance hydration without stress or guesswork.
  • Shaping and texture guidance – Whole grain doughs have a mind of their own, but with a few small shifts, you can create loaves that are soft inside, crisp outside, and distinctly yours.
  • Practical tips from experience – Every insight here comes from my own 25+ years of working with sourdough and fresh flour, what’s worked, what hasn’t, and how you can skip the trial and error to bake with calm, steady confidence.

What Is Freshly Milled Flour?

Freshly milled flour is whole grains, like wheat berries, ground at home just before baking. Because it hasn’t been processed or sitting on a store shelf, it keeps its natural oils, aroma, and texture, which makes it feel more alive in your dough.

You’ll notice it behaves differently than bagged flour. It absorbs more water, ferments faster, and gives your sourdough a rustic, full-bodied character that feels homemade in the best way.

It can take a little time to adjust, but once you learn its rhythm, you’ll find it brings a deeper connection between the grain in your jar and the loaf on your table.

Some bakers prefer to sift out larger bran pieces, while others use the flour exactly as it is. There isn’t a wrong approach here, only what works best for your kitchen and your bake. To learn more about sifting read this guide: How to Sift Freshly Milled Flour | When & Why It Matters.

If you’re just getting started, you can these guides to learn more: Tools for Milling Flour at Home | Mills, Mixer, & More can help you set up, and Best Whole Grains to Mill for Baking Bread & More ,will give you a clear idea of which grains work best for different bakes.

Tips for Sourdough & Fresh Milled Flour Challenges

Hydration feels tricky – Freshly milled flour absorbs more water than bagged flour. Start with a slightly higher hydration than usual, and give the dough time to rest so the flour can fully absorb the liquid before you shape or mix again.

Fermentation moves faster – Whole grain flour is naturally active, so your dough will often rise more quickly. Watch the dough, not the clock, and be ready to shorten bulk fermentation if things are moving fast.

Loaves feel dense – Because fresh flour contains the bran and germ, it can weigh your dough down. Try sifting part of the flour through a fine sieve (#40 or #50), or blend in a little store-bought flour while you learn.

Replacing all-purpose flour – You can swap all-purpose for freshly milled flour, but expect a change in texture. All-purpose is softer and more refined, while fresh flour brings a heartier flavor and structure. Adjust hydration and fermentation times to fit your bake.

Avoiding beginner mistakes – The most common hurdle is treating fresh flour exactly like store-bought. Instead, think of it as its own ingredient. Give it more water, expect a quicker rise, and don’t be afraid to experiment as you get comfortable.

Note: If you’re new to baking sourdough, begin with a strong, healthy starter — it’s the heart of every successful bake. You can use a traditional starter made with store-bought flour or a lively one built from freshly milled grain. To learn how, explore these two step-by-step guides: How to Make a Sourdough Starter | A Beginner’s Guide and for a freshly milled flour starter: How to Make A Freshly Milled Flour Sourdough Starter.

How to Use Sourdough with Freshly Milled Flour

If you’ve only baked with bagged flour before, freshly milled flour will feel like a whole new ingredient. It’s full of natural oils and textures that make your dough ferment faster and absorb water differently. You may need to adjust your process a little, but the results are absolutely worth it.

  1. Try sifting (or not) –  Using a fine sieve (#40 or #50) can remove the largest bran pieces that sometimes cut into the gluten structure. Don’t toss the bran — it’s wonderful for dusting banneton baskets, coating loaves, or stirring into muffins and pancakes. As you gain confidence, you may find you prefer skipping the sifting altogether, especially for rustic or whole-grain loaves.
  2. Consider a soak – If you’d rather not sift, soften the bran by soaking the flour with warm water before mixing your dough. This makes the flour easier to handle and helps you achieve a more consistent hydration.
  3. Add salt early or after autolyse –  Some bakers hold off on adding salt, believing it slows fermentation, but it actually depends on your dough and timing. Salt naturally tightens gluten and steadies fermentation, giving you a dough that’s easier to handle and less likely to overproof — especially with freshly milled flour. You can add it early to build structure from the start or wait until after your autolyse for a gentler rise. Either way, find the rhythm that fits your kitchen and your dough’s personality.
  4. Expect faster fermentation – Whole grains bring extra life to your dough. Don’t be surprised if bulk fermentation moves more quickly than you’re used to. Focus on watching your dough’s texture and rise, not the clock, to build strength and volume with confidence.
A little note

If you’d like more guidance on balancing hydration or adapting your recipes, read How to Convert Recipes to Freshly Milled Flour. It walks you through how to make any recipe work beautifully with your home-milled flour.

Low-Maintenance Refrigerator Starter Routine (No Waste)

This low-maintenance refrigerator starter routine was passed down from my grandmother, and I’ve kept it going in my own kitchen ever since. It’s a steady, no-waste method that keeps your starter strong without daily feedings — and now, I’m passing it on to you.

  • Feed more flour than water – Refresh your starter with about 1 cup of flour and ½ cup of water, stirred into roughly 30 g of leftover starter. A thicker feed slows fermentation so the starter stays active longer in the fridge.
  • Let it sit briefly – After feeding, let the jar rest on the counter for 1–2 hours, just until you see gentle bubbling and the first signs of life. Then it’s ready to chill.
  • Store it cold – Move the jar straight to the refrigerator, where it will ferment slowly through the week. Because the flour isn’t fully consumed, the starter keeps plenty of stored energy, meaning there’s no daily discard to manage.
  • Use as needed – When a recipe calls for starter, scoop out only what’s needed and build from that amount. For example, if you need 2 cups for several loaves, feed just enough to make that yield. Nothing extra, nothing wasted.
  • Re-feed weekly – Refresh the jar once a week using the same routine: more flour than water, a short counter rest, then back into the fridge. This keeps your starter strong, consistent, and ready whenever you bake.
  • Sift for strength –Sifting the flour with a #40 sieve before feeding removes coarse bran that can interfere with gluten development, making it easier to tell when the starter is at its peak.
  • Skip rye flour unless you need it – Rye flour speeds fermentation quickly, which can make the starter rise fast and collapse. Unless your recipe calls for it, use a mix of unbleached all-purpose flour and freshly milled flour instead for a steadier rise and balanced flavor.

NOTE: This low-maintenance refrigerator starter routine comes from my grandmother’s kitchen — a tradition that’s kept our starters alive for generations. It’s a steady, no-waste method that keeps your starter strong without daily feedings, and now I’m passing it along to you to make it part of your own sourdough rhythm at home.

Equipment for Baking Sourdough with Fresh Milled Flour

Here are the basics you’ll need to get started. If any of these terms feel new, check out this resource: Glossary Of Terms For Sourdough & Freshly Milled Flour

  • Banneton basket – Used for shaping and proofing your dough so it holds its form and develops that rustic pattern we all love.
  • Dutch oven – Creates the steam your bread needs for a crisp crust and tall oven spring.
  • Lame or sharp knife – Helps you score the dough just before baking, guiding how the loaf expands in the oven.
  • Parchment paper – Makes transferring your dough into the hot Dutch oven smooth and stress-free.
  • Sourdough starter – The living heart of your bread, fed and ready to bring rise and flavor to every loaf.
  • Flour, water, and salt – The foundation of every bake. Keep them fresh and measured for consistent results.
  • Mixing bowl – A sturdy bowl for mixing and rising. Choose one that feels comfortable to work with.
  • Danish whisk or wooden dough whisk – Gently blends flour and water without overworking your dough.
  • Cover for the bowl – A damp tea towel, clean shower cap, or bit of plastic wrap keeps your dough from drying as it ferments.
A chocolate cake with a slice served on a floral plate.

Sourdough Recipes for Freshly Milled Flour

Freshly milled flour brings warmth, depth, and life to both sweet and savory bakes. These recipes are reader favorites from my own kitchen — tested, loved, and shared by home bakers learning to bake with fresh flour.

Cottage Miller’s Note

Baking sourdough with freshly milled flour is a rhythm — one that blends patience, curiosity, and the quiet satisfaction of watching something living rise in your own kitchen. Every loaf you bake brings you a step closer to understanding your grain by heart.

If you’d like to keep learning, you’ll find a full collection of milling and baking tutorials inside The Cottage Mill. From where to buy wheat berries to how to store, sift, and troubleshoot, the series includes fifteen step-by-step guides that walk you through every part of the process — from grain to golden loaf.

The Cottage Mill

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FAQ

Starter feeding stays the same. But because fresh flour ferments faster, you may find your starter peaks sooner. Watch for the bubbly, stretchy “double in size” stage, not just the clock. To learn how to make a Freshly Milled Flour Starter read this post: How to Make A Freshly Milled Flour Sourdough Starter.

Not necessarily. A grain mill gives you fresher flour, but you can use freshly ground flour from a high‑speed blender or a grain mill attachment. For simple setups, the goal is freshness and quality—not the tool itself. To learn more about what milling tools I suggest read this post: Tools for Milling Flour at Home | Mills, Mixer, & More.

You can, but sifting removes large bran bits that may “cut” gluten. If you do sift, you can reintroduce the bran later for flavor—or use it for banneton dusting, discard recipes, or breakfast bakes. To learn the ins and outs all about sifting freshly milled flour read this guide: How to Sift Freshly Milled Flour | When & Why It Matters.

Freshly milled flour contains more natural oils and active bran particles, which absorb liquid differently than store-bought flour. That’s why your dough may feel stiffer or drier at first. Add water a tablespoon at a time until the dough feels soft, elastic, and slightly tacky. The goal isn’t to hit a number, but to find the texture that feels alive in your hands.

Fresh flour speeds fermentation, so rely on feel, not time. Look for a slight dome in your loaf or gentle jiggle when poked. Overproofed dough won’t spring well in the oven—even if it looks puffy on the surface.

Yes, absolutely. Mixing the two can make the transition smoother while you adjust to fresh flour’s texture and hydration. Start with a 50/50 blend, then increase your freshly milled flour as you get comfortable. To learn more read this guide: How to Convert Recipes to Freshly Milled Flour.

Start small—try 20–50% fresh milled flour blended with your usual flour. That helps you adjust hydration and fermentation without overwhelming your dough. Over time, you can increase as you learn how it affects texture and rise. To learn more read this guide: How to Convert Recipes to Freshly Milled Flour.

Yes — freshly milled whole-grain flour contains more active enzymes and natural oils than standard flour, which can speed up fermentation and break down gluten if the dough is left too long.

To prevent your loaf from turning flat or collapsing, keep a closer eye on your dough’s rise. Consider shortening bulk fermentation, using cooler temperatures, or lowering hydration slightly. The goal is to balance flavor and rise — not to race the clock.

A wooden flour mill dispensing freshly ground flour into a glass bowl in a cozy kitchen with copper utensils.

Step into The Cottage Mill: Freshly Milled Flour Guides, Recipes, and More Await!

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Milling Essentials

  • Sieve Fine Mesh
  • Multi-layer electric flour sifter with brush and sieve accessories, perfect for refining freshly milled flour for lighter baking.
    Sidasu Automatic Vibrating Sieve Shaker
  • WonderMill electric grain mill with flour container, wheat berries, and milled flour—an essential tool for home flour milling.
    Wondermill Grain Mill
  • Digital kitchen scale with a bowl of sliced almonds on top, displaying the weight on the LCD screen.
    Digital Kitchen Scale
  • Copper measuring cups and spoons with wooden handles, displayed with coffee beans and spices, ideal for accurate and beautiful baking prep.
    Copper Stainless Steel Measuring Cups and Spoons

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    More Freshly Milled Flour Guides

    Thank you for spending time with me here at The Modern Day Cottage. My hope is that each guide helps you mill and bake with more confidence. May your jars be ever full, and your loaves rise high.
    With love & gratitude,
    Emily

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    Close-up of a woman in a peach blouse smiling and leaning against a kitchen counter, with fresh flour and wheat berries visible beside her.

    Emily Rider

    Cottage lifestyle blogger and home miller with 25+ years of sourdough and fresh-milled flour experience.
    Sharing cozy homemade recipes that help you bake with confidence, celebrate each season, and savor the beauty of everyday cottage living.

    About Me

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