How to make 100% Whole Wheat Sourdough at Home.

Last updated on February 10th, 2025 at 06:11 pm

Fresh Milled 100% whole wheat sourdough is one of my favourite breads to bake. It’s nutritious, flavourful, and deeply satisfying, with a slightly nutty taste and a hearty texture. While working with whole grains can be challenging, the reward is a loaf that’s both wholesome and delicious—perfect for everyday sandwiches, toast, or just enjoying with butter.

Why Bake 100% Whole Wheat Sourdough?

Baking with 100% whole wheat sourdough is a unique challenge—rewarding, exciting, and sometimes frustrating. Whole grains behave differently than white flour, requiring extra attention to hydration, fermentation, and gluten development.

This is not a beginner-friendly recipe. If you’re new to sourdough, I recommend starting with my Beginner’s Sourdough Guide before tackling this loaf. But if you’re ready to level up your baking skills, this recipe will teach you how to work with whole wheat, develop incredible flavour, and bake a truly wholesome loaf.

How I Mastered 100% Whole Wheat Sourdough: Lessons from a Vermont Bakery

In 2016 after leaving my position as Sous Chef at Cafe Boulud in the Four Seasons Toronto, I needed a break from cooking. I decided that I wanted to stage (a free work term) in a bakery to get a better understanding of whole grains. After looking at some of the top bakeries in North America, I found a little bakery in Vermont called Elmore Mountain Bread that would forever change my life. It was here that I developed a new understanding and passion for baking with organic grains that are freshly milled into flour. Blair and Andrew helped me understand the differences in working with fresh milled flour and how I could utilize them in my home baking.

Why 100% Whole Wheat Sourdough Ferments Faster & Bakes Differently

Whole wheat flour behaves very differently from white flour in sourdough baking. It ferments faster, absorbs more water, and produces a denser loaf with less volume. That’s why many sourdough recipes only include 20 to 30 percent whole wheat, but this recipe is truly 100 percent whole wheat sourdough.

Over the years, I’ve tested different techniques, including sifting and scalding the wheat, to improve texture and fermentation. After countless bakes, I’ve finally settled on a formula that balances hydration, fermentation, and structure to create a soft, flavourful, and well-risen whole wheat sourdough loaf.

Flavour, Health, and Starter Technique

This bread has an exceptional flavour without the bitterness that can sometimes be found in 100 percent whole wheat sourdough. While much of this comes down to the quality of the grains, the formula and fermentation schedule also play a key role.

Since I work around baked goods almost every day, I prefer to make breads with higher percentages of whole grains as my go-to daily loaves for my family. Many bakers focus on achieving an open crumb, but in my opinion, this loaf is more challenging, more rewarding, and—most importantly—healthier.

You can make this bread with a standard sourdough starter, but I prefer to use a 100 percent whole wheat starter at 65 percent hydration to keep the loaf true to its name. If you don’t have one, you can easily convert your existing starter by gradually feeding it whole wheat flour instead of white. Just keep in mind that it will ferment a little differently, as whole wheat tends to be more active and faster to rise.

Another option is to build your levain using a white starter and whole wheat flour, which still produces great results. But if you want to keep things as pure as possible—and earn some extra bragging rights—a 100 percent whole wheat starter ensures there’s barely any white flour in the final loaf.

The Importance of Flour

The type of flour you use plays a crucial role in the success of 100 percent whole wheat sourdough. I use 100 percent organic hard red spring wheat kernels, milled finely on a New American Stone Mill. Canadian wheat is known for its strength, and the specific flour I use has the following specs:

• 100% organic hard red spring wheat
• 12.5% protein (helps with gluten development)
• 1.6 – 1.8% ash content (higher mineral content contributes to flavour and fermentation)

For the best results, I recommend using stone-milled whole wheat flour with a high protein percentage. If you’re unsure about your flour’s strength, you can test its hydration capacity:

1. Mix 50 grams of flour with 45 grams of water (about 85–90% hydration).
2. Let it rest for one hour to fully absorb the water.
3. Stretch the dough gently—if it holds together well and has elasticity, your flour has good strength. If it feels weak or tears easily, you may need to adjust hydration in your final dough.

How Flour Milling Affects Hydration & Fermentation

The way your whole wheat flour is milled directly impacts hydration, fermentation, and gluten development. Here’s what I’ve found through experience:

• Finer-milled flour absorbs more water – The finer the flour, the better it hydrates, leading to a softer dough.
• Coarse bran can weaken the gluten network – Large bran particles can cut through gluten strands, making the dough more fragile.
• Komo & Mockmill flours absorb less water – If you’re milling at home using a Komo or Mockmill, expect your dough to require less hydration than flour milled on a New American Stone Mill or similar high-end mills.
• Sifting can help – If your flour has a lot of coarse bran, consider sifting out some of it and using it to dust your bannetons instead. This helps maintain structure while still keeping the benefits of whole wheat.

Want to learn more about milling your own fresh flour? Check out my complete guide here.

Hydration & Fermentation Considerations

• Watch your dough temperature – Since this dough is both whole grain and high hydration, it can over-ferment if left too warm for too long. Keep an eye on it and adjust accordingly.
• Whole grain flours ferment faster – They contain more nutrients, which feeds the wild yeasts in your sourdough starter and speeds up fermentation.
• Higher hydration = faster fermentation – Doughs with higher water content tend to ferment more quickly, so be mindful of bulk fermentation times.

100% Whole Wheat Levain Sourdough Specs

Total Formula

This is the total of all the ingredients needed to make this 100% whole wheat sourdough recipe.

If you want to scale this recipe easily and change the amount of loaves or loaf size, you can download my 100% whole wheat sourdough dough calculator.

100% Whole Wheat Sourdough Dough Schedule

To make the process easier, I’ve created a sourdough schedule to help guide you through each step. Keep in mind, this is just a framework—the dough is always the boss. Factors like room temperature, flour type, and fermentation strength can all affect timing, so use this as a reference but pay attention to how your dough behaves.

Mix the 100% Whole Wheat Stiff Levain – 9:00 am

If you don’t regularly keep a whole wheat starter, you can still use your standard sourdough starter to build this levain. I prefer a stiff levain at 65 percent hydration, which may feel quite different if you’re used to working with a liquid levain.

While I recommend using a stiff levain for this dough, a liquid starter will work as well—just keep in mind that it will increase the overall hydration of the final dough, which may require slight adjustments.

Note: This build has a 50g levain buffer built in to help perpetuate the starter.

I prefer to mix the levain in a bowl first before transferring it to a jar. Since this is a relatively low-hydration levain, mixing it thoroughly in a bowl ensures everything is well incorporated.

1. Add your 26°C water and sourdough starter to a bowl and mix until combined.
2. Add the flour and knead the mixture into a firm ball.
3. Transfer it to a jar and place an elastic band at the top level of the levain to track its rise.
4. Store the jar in a warm place (26°C/80°F) and allow it to ferment.

How to Tell When Your Stiff Levain is Ready

A fully ripe stiff levain will have:

• A domed top that has not yet collapsed
• Tripled in volume (use the elastic band to track growth)
• A strong egg-like smell when broken open

This process typically takes three to four hours, depending on your environment and starter activity.

I first learned this stiff levain build from German Master Baker Michael Schulze, and it has proven to be incredibly effective for high whole grain or high hydration doughs that need extra strength.

(The video below shows a ripe levain just before mixing the dough.)

Autolyse – 10:00am

I’ve experimented with autolyse times ranging from one to six hours, and for 100 percent whole wheat sourdough, I find the best results come from a 90- to 120-minute autolyse.

• Too short (less than 90 minutes) – The flour doesn’t fully absorb the water, leading to a stiff, less extensible dough that is difficult to fold and shape.
• Too long (over two hours) – The gluten network actually weakens, making the dough more fragile and harder to handle.

For this recipe, a 90- to 120-minute autolyse provides the right balance, allowing the flour to hydrate properly while maintaining enough gluten strength for shaping.

Autolyse Process

1. Add the flour to a large mixing bowl or the bowl of a stand mixer.
2. Pour in 735 grams of water and mix until fully combined, ensuring there are no dry bits of flour.
3. Cover the bowl and let the dough rest in a warm place, ideally at the same temperature as your levain (around 26°C/80°F).

Important: This autolyse is done without the levain and salt. These will be added later to maintain proper fermentation control and gluten development.

Mix the Whole Wheat Sourdough – 12:00 pm

Incorporating the Stiff Levain & Mixing the Dough

1. Mixing in the Levain

• Break up the stiff levain into small pieces and distribute it over the dough.
• Add half of the remaining water to help incorporate the levain.
• Mixing options:
  • By hand – Mix for about 10 minutes, using your hand like a claw to pinch the levain into the dough.
  • Spiral mixer – Mix on first speed for 5 minutes.
  • Planetary or KitchenAid mixer – Mix on low speed for 7 minutes.

2. Strengthening the Dough

• Once the levain is fully incorporated, take one corner of the dough and stretch it over itself.
• Continue stretching and folding around the bowl until the dough feels strong.
• Cover and let the dough rest for 5 minutes.

3. Adding Salt & Final Mixing

• After resting, add the remaining water and salt to the dough.
• Mixing options:
  • Spiral mixer – Mix on first speed for 5 minutes.
  • Planetary/KitchenAid mixer – Mix on low speed for 7 minutes.
  • By hand – Mix for 10 minutes, incorporating fully.
• Let the dough rest for another 5 minutes before doing a final mix.

4. Final Mix & Gluten Development

• Final mixing:
  • Spiral mixer – Mix on second speed for 5 minutes.
  • Planetary/KitchenAid mixer – Mix on medium speed for 6 minutes.
  • By hand – Mix for 10 minutes.
• This extra mixing strengthens the gluten network, helping the dough hold its shape and rise properly.

Why Proper Mixing Matters

• Proper mixing ensures the bubbles have strong, elastic walls, resulting in a well-risen, airy 100% whole wheat sourdough loaf.
• Think of the air bubbles in the dough like balloons.
• As the dough expands, these bubbles stretch—if the gluten isn’t well-developed, the walls will collapse under the weight of the coarse bran.

Desired Dough Temperature – 24°-25C/75.2-77°F

I prefer to keep this dough on the cooler side, as 100 percent whole wheat ferments quickly and can easily overproof if left unchecked. Maintaining a dough temperature of 24°–25°C (75.2°–77°F) helps control fermentation speed, allowing for better gluten development and structure.

Monitor the dough temperature throughout bulk fermentation to ensure it stays within this range—too warm, and fermentation may get away from you.

Learn more about controlling fermentation in my guide on Desired Dough Temperature (DDT).

Bulk Fermentation 12:30 pm – 4:00 pm

I keep bulk fermentation for 100 percent whole wheat sourdough between 3 to 3.5 hours, slightly cooler than my typical range. While I usually ferment between 26°–28°C (79°–82°F), I find that 24°–26°C (75°–79°F) works better for this dough. Whole wheat and fresh-milled flour ferment very quickly, so a slightly lower temperature helps maintain structure and prevents overproofing.

How to Bulk Ferment:

• Transfer the dough to a dough tub or bowl immediately after mixing.
  • Small batches (2 loaves): A ceramic bowl helps retain consistent temperature.
  • Larger batches: A Cambro container works well for fermentation control.

• Let the dough rest for 60 minutes before performing the first fold.
• Perform 3 sets of folds at the 60, 90, and 120-minute marks:
  • Using wet hands, stretch the dough up and fold it over itself.

• Final stretch & fermentation check:
  • After the last fold, let the dough relax for the remainder of bulk fermentation.
• If the dough feels slack, add an extra fold at 150 minutes, but allow time for the dough to rest before shaping.

End of Bulk Fermentation: What to Look For

At the end of bulk fermentation, the dough should have increased in volume by 30 to 40 percent. Unlike white flour sourdough, 100 percent whole wheat dough won’t achieve the same dramatic rise, so it’s important to rely on visual and textural cues rather than expecting it to double.

Since whole wheat sourdough can be more challenging to work with, pay close attention to how your dough feels—it should be slightly puffy, well-aerated, and strong enough to hold its shape. If it feels weak or overly slack, it may need a slight adjustment in fermentation time.

Divide and Preshape – 4:00 PM

1. Turn the dough out onto your work surface—no flour is needed, but if sticking is a concern, lightly dust with whole wheat flour.
2. Divide the dough in half using a bench scraper.
3. Preshape into rounds:
   • Hold the scraper in one hand and the dough in the other.
   • Pull the dough across the table, stretching it into a round shape.
   • If the dough sticks to your hands, lightly flour them, but a well-developed dough shouldn’t need it.
4. Rest uncovered for 30–45 minutes.
   • Allowing the dough to sit uncovered helps dry the surface slightly, making final shaping easier.

Final Shape – 4:45 PM

If this is your first time making 100 percent whole wheat sourdough, I highly recommend shaping it as a boule rather than a batard, as it is much easier to handle.

How to Shape the Dough

1. Lightly flour the top of the dough and flip it over onto the work surface.
2. Form a tight package:
   • Bring the bottom up and seal.
   • Stretch the sides out and fold them into the center.
   • Fold the top down about one-third of the way and tuck the sides in.
3. Roll the dough lightly to create an oval shape.

Transferring to the Banneton

1. Let the shaped dough rest on the table for 2–3 minutes to relax.
2. Flip it over and place it seam-side up into a banneton.
3. Dusting the banneton:
   • I use a mix of rye flour, rice flour, and coarse bran to prevent sticking and enhance the texture of the crust.
   • You can also use only rice flour if preferred.

Cold Fermentation & Final Proof – 5:00 PM to 8:30 AM

1. Let the shaped dough rest in the banneton for 10 minutes, covered in a reusable bag.
   • I prefer using a clear plastic shopping bag that can be reused.
2. Transfer the dough to the fridge at 3°C (38°F) for an overnight cold fermentation.

Why Cold Fermentation Matters

• Slows down fermentation – Whole wheat ferments quickly, so chilling it prevents overproofing.
• Enhances flavour – A longer fermentation develops deeper, more complex flavours.
• Strengthens the dough – The cold temperature makes it easier to handle and score before baking.
• Prevents excessive acidity – Over-fermenting in the fridge can cause too much acidity, weakening the gluten.

For the best results, bake the dough after 10–14 hours of cold fermentation. This dough is ready to bake straight from the fridge—no need for it to come to room temperature.

Baking – 8:30 AM to 9:30 AM

1. Preheat the Dutch Oven

• Place your Dutch oven (lid on) inside the oven and preheat to its maximum temperature for about one hour.
• I use a Challenger Bread Pan, but any Dutch oven will work.

2. Prepare the Loaf for Baking

• Remove the preheated Dutch oven from the oven and take the lid off.
• Place a pre-cut piece of parchment paper inside the pan.
• Gently flip the loaf out onto the parchment paper.

3. Score the Dough

• Using a lame at a 45° angle, score the top of the loaf to control expansion during baking.

4. Create Steam for a Better Crust

• Place the lid back onto the Dutch oven, leaving a small crack open.
• Spray about 15 spritzes of water onto the lid before sealing.
• Alternatively, you can add a cube of ice to the pan, but I prefer spraying water for better steam control.

5. Bake the Loaf

• Place the Dutch oven back into the oven and immediately lower the temperature to 243°C (470°F).
• Bake for 22 minutes with the lid on, then remove the lid and bake for another 14 minutes.
• If the loaf is browning too quickly, reduce the temperature to 232°C (450°F) for the final 10 minutes of baking.
• Keep in mind that every oven bakes differently, so adjust times and temperatures as needed.

6. Cooling & Slicing

• Remove the loaf from the oven and tap the bottom—it should sound hollow, indicating it’s fully baked.
• Transfer the loaf to a cooling rack and allow it to cool completely before slicing.
• It’s tempting to cut into it right away, but waiting at least an hour ensures the crumb sets properly and prevents a gummy texture.

Frequently Asked Questions

1. Can I make this recipe without a stiff levain?

• Yes! While a stiff levain (65% hydration) helps with structure, you can use a liquid starter (100% hydration). Just reduce the water in the main dough slightly to maintain balance.

2. Why is my whole wheat sourdough dense?

100% whole wheat bread has less gluten strength than white flour. To improve the texture:

• Make sure your starter is active and bubbly before mixing.
• Don’t rush fermentation—a long, slow proof helps develop structure.
• Try using a slightly higher hydration if your flour can handle it.

3. Can I cold ferment the dough for longer than 12-14 hours?

• Yes! You can cold-proof for up to 24 hours, but beyond that, the dough may over-ferment, leading to excessive acidity and gluten breakdown.

4. What’s the best way to store whole wheat sourdough?

Once fully cooled, store it:

• At room temperature: Wrapped in a linen bread bag or paper bag (up to 3-4 days).
• In the freezer: Sliced and wrapped in plastic or a freezer-safe bag (up to 3 months).

For a full guide on keeping your bread fresh, check out How to Store Sourdough Bread.

5. Can I use store-bought whole wheat flour instead of fresh-milled?

• Yes! Fresh-milled flour has more active enzymes and flavour, but store-bought stone-ground whole wheat flour works well. Just adjust hydration as store-bought flour absorbs water differently.

100% Whole Wheat Sourdough Final Thoughts

This dough took me many attempts to perfect, so don’t be discouraged if it doesn’t turn out exactly right on your first try. 100 percent whole wheat sourdough can be challenging, but with patience and practice, you’ll develop a feel for how the dough behaves.

When first trying this formula, avoid pushing the hydration too high—the exact amount of water your dough can handle depends on your flour. I use very strong Canadian wheat, which can hold more water and stand up to long fermentation. If you want to play it safe, start with 75 percent whole wheat and 25 percent bread flour, but keep in mind that bread flour absorbs less water than whole wheat.

The result is absolutely worth the effort—this bread is flavourful, hearty, and free from the dense texture or bitterness that many 100 percent whole wheat sourdoughs can have. It has become a staple in our household, and I hope it will in yours too.

If you’d like to get weekly sourdough tips, tricks, and recipes, you can join my newsletter here and for those who want to fine-tune their baking, check out my 100% Whole Wheat Sourdough Calculator.

More Artisan Bread Recipes to Try

Looking to expand your sourdough baking? Here are some other great recipes to explore:

• Turmeric Sourdough (A vibrant loaf packed with warm, earthy flavours.) – Check out the recipe
• 100% Rye Sourdough (Video tutorial) – Watch on YouTube
• Whole Wheat Tangzhong Milk Buns (Not sourdough, but an incredible soft whole wheat bread!) – Get the recipe
• Multigrain Sourdough (Perfect for adding texture and flavour to your loaves.) – Learn how to make it
• Jalapeño Cheddar Sourdough (A spicy, cheesy variation for a bold flavour.) – Try it here

100% Whole Wheat Sourdough Recipe Card

100% Whole Wheat Sourdough

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4.9 from 7 reviews

• Author: Matthew James Duffy
• Total Time: 4 hours 40 minutes
• Yield: 2 loaves 1x

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Description

Fresh milled 100% whole wheat sourdough is a deeply flavourful and hearty loaf, perfect for everyday baking. Made with just four simple ingredients—whole wheat flour, water, salt, and sourdough starter—this naturally leavened bread has a rich, nutty taste and a satisfying chew. While whole wheat sourdough can be challenging, this step-by-step guide will help you master hydration, fermentation, and shaping to achieve a well-risen, beautifully textured loaf. Whether you enjoy it toasted with butter or as the base for a sandwich, this wholesome sourdough is a must-bake for any bread enthusiast.

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Ingredients

Scale 1x2x3x

For the Levain:

• 53g whole wheat flour
• 34g water (26°C/80°F)
• 69g mature sourdough starter

For the Dough:

Autolyse:

• 864g whole wheat flour
• 735g water (26°C/80°F)

Mix In:

• 50g water
• 19g salt
• 106g stiff whole wheat levain (from the above build)

Cook Mode Prevent your screen from going dark

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Instructions

For the Levain:

1. Mix 53g whole wheat flour, 34g water (26°C/80°F), and 69g mature sourdough starter until well combined.
2. Let rise for 3–4 hours in a warm place (26°C/80°F) until tripled in volume.

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For the Dough:

Autolyse:

1. Add 864g whole wheat flour to a large bowl or mixer.
2. Pour in 735g of water (26°C/80°F) and mix until fully incorporated, leaving no dry bits.
3. Cover and leave in a warm place, ideally the same temperature as your levain.

Mix In:

1. Break up the stiff levain over the dough.
2. Add half of the remaining water (25g) and mix well. Let rest for 5 minutes.
3. Add the salt (19g) and remaining 25g of water and mix until fully combined.
4. Let the dough rest for 5 minutes.
5. Mix the dough until well developed.

• Desired Dough Temperature (DDT): 24°-25°C (75.2°-77°F)

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Bulk Fermentation:

1. Allow the dough to bulk ferment at 24°-25°C (75.2°-77°F) for 3–3.5 hours.
2. Perform 3 sets of folds at the 60, 90, and 120-minute marks.

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Pre-Shape:

1. Using a bench knife, divide the dough into 2 equal pieces.
2. Pre-shape each dough into a round ball.
3. Rest uncovered for 30-45 minutes.

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Final Shape:

1. Lightly flour the top of the dough and flip it over onto the work surface.
2. Bring the bottom up and seal.
3. Stretch the sides out and fold them into the center to create a tight package.
4. Bring the top down about ⅓ of the way, pulling the sides in.
5. Gently roll the dough to give it an oval shape.
6. Allow the dough to rest for 2–3 minutes, then flip it over and place it into a banneton seam-side up.
7. Let the dough rest for 10 minutes before covering and placing it into the fridge.
8. Cold ferment for 10-14 hours at 3°C (38°F).

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Baking:

1. Place your Dutch oven (lid on) inside the oven and preheat to its max setting (500°F/260°C) for 1 hour.
2. Remove the preheated Dutch oven and take the lid off.
3. Place a pre-cut piece of parchment paper inside the pan.
4. Gently flip the loaf out onto the parchment paper.
5. Using a lame at a 45° angle, score the bread.
6. Place the lid back onto the Dutch oven, leaving a small crack open.
7. Spray 15 spritzes of water onto the lid before sealing.
8. Place the Dutch oven back into the oven and immediately lower the temperature to 243°C (470°F).
9. Bake for 22 minutes with the lid on, then 14 minutes with the lid off.
10. Remove the loaf from the oven and allow it to cool completely before slicing.

Notes

• Hydration Tip: Whole wheat absorbs more water, but different flours hydrate differently. Start with slightly lower hydration if unsure.
• Temperature Matters: A slightly cooler fermentation (24-26°C) prevents overproofing.
• Cold Fermentation Benefits: Enhances flavour, makes scoring easier, and extends dough shelf life before baking.
• Flour Choice: Use strong whole wheat flour with at least 12.5% protein for best gluten development.
• Best Results: Bake straight from the fridge—no need to let the dough come to room temperature.

• Prep Time: 4 hours
• Cook Time: 40 minutes
• Category: Sourdough
• Method: Natural Fermentation & Baking
• Cuisine: Baking