This Whole Wheat Sourdough Focaccia is made with 100% whole wheat flour but still comes out soft and bubbly thanks to its high hydration. Whether you make it the same day or ferment overnight, it’s wonderfully tangy with a hearty texture and nutty flavor.

Several pieces of whole wheat sourdough focaccia on a piece of wrinkled parchment paper.

Whole wheat flour can be tricky to work with, but I love the challenge of creating 100% whole wheat sourdough recipes. After sharing my classic sourdough focaccia, I knew I had to try a whole wheat version.

While I was testing this recipe, we had some friends over for a board game night. So I decided to serve the focaccia with homemade marinara sauce for dipping. They absolutely loved it, and it was the perfect snack for the evening!

This whole wheat sourdough focaccia is soft, bubbly, and tangy - especially if fermented overnight. The whole wheat flour adds a hearty texture and nutty flavor, while the olive oil creates a beautifully crispy crust.

Don't be intimidated by whole wheat flour or the 100% hydration dough. With a few simple techniques - like autolysing, using a strong starter, and building gluten through stretch and folds - this focaccia is actually quite easy to make.

I really hope you give it a try and enjoy it as much as I did!

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Ingredients & Substitutions

Here are some notes on key ingredients. For a full list of ingredients, check out the recipe card below.

Sourdough Starter- You can use either an active sourdough starter or discard for this focaccia. If using discard, choose some that’s less than a week old to help the dough rise well.
Whole Wheat Flour- This focaccia is made with 100% whole wheat flour, giving it a hearty flavor and chewy texture. If you prefer a softer crumb, you can swap some of the whole wheat for bread or all-purpose flour.
Water- This dough is high hydration (100% water), which helps create a light and airy focaccia with those signature large bubbles. At first, it might feel more like a thick batter, but after a few sets of stretch-and-folds, you’ll notice it gains structure.
Olive Oil- Adds flavor and keeps the focaccia from sticking to the pan. Use the best extra virgin olive oil you have on hand, and don’t skip drizzling some on top before baking!
Kosher Salt- Salt brings out the flavor in the dough and the toppings. I like to sprinkle extra on top for that perfect salty bite. I use Diamond Crystal Kosher Salt (about 2.8 grams per teaspoon). If you’re using table salt or Morton’s, measure by weight or use half the amount.
Herbs & Toppings- Rosemary is a classic choice, but feel free to get creative. Try thyme, oregano, or a mix of fresh herbs. Add thinly sliced garlic, cherry tomatoes, or even caramelized onions for extra flavor.

The ingredients to make whole wheat sourdough focaccia. Each ingredient is labeled with text. They include whole wheat flour, kosher salt, olive oil, water, and sourdough starter.

Choosing the Size of Your Baking Pan

Choosing the size of your baking pan will depend on your preference for the thickness and texture of your focaccia. Here are a few options to help you decide:

9"x13" Baking Pan: Ideal for a thicker focaccia with crispy edges and a soft, fluffy interior.
Half Sheet Pan (18"x13"): Produces a thinner focaccia with more crispy edges - perfect for making sandwiches!
Two 8"x8" Square Pans: Great for making thicker focaccia and experimenting with different toppings on each.

Tips for Success

Use active starter. Whole wheat flour doesn’t rise as high as bread flour due to the bran and germ, so it’s important to use a strong, active starter or fresh discard for the best rise and structure.
Don't skip the autolyse. Autolysing is key when using whole wheat flour. Letting the dough rest after mixing the flour and water helps soften the bran and germ, giving the gluten a head start and resulting in a lighter, fluffier focaccia.
Wet your hands. This dough is high hydration and sticky, so keeping your hands wet will prevent sticking and make stretching and folding much easier.
Line the pan with parchment paper. This adds an extra layer of insurance against sticking and makes cleanup a breeze.
Proof overnight for more flavor. If you’re a fan of that bold sourdough tang, pop the dough in the fridge overnight after spreading it into the pan.
Get creative with toppings. Focaccia can be topped with just about anything you'd like! Try it with garlic and garden-fresh vegetables, or turn it into a focaccia pizza with tomato sauce and cheese.

How to Make Whole Wheat Sourdough Focaccia

Here's how to make a delicious sourdough focaccia using 100% whole wheat flour.

1. Feed Starter

Feed your sourdough starter 6-12 hours before starting the dough to make sure it’s bubbly and active.
It will take around 6 hours if your kitchen is warm (75°F) or closer to 12 hours if it’s cooler (65-68°F).

An active sourdough starter in a glass mason jar.

2. Autolyse

In a large bowl, combine the whole wheat flour and warm water. Stir until no dry flour remains.
Cover and let it rest for 1 hour.

Whole wheat flour and water autolysing in a bowl.

3. Mix Dough

After the 1-hour autolyse, add your sourdough starter and salt to the bowl. Mix everything together by hand until a sticky, wet dough forms.
Cover and let it rest for 15 minutes.

Sourdough starter and kosher salt added to the flour and water in a bowl.

Whole wheat sourdough focaccia dough in a mixing bowl.

4. Stretch and Folds

Wet your hand to prevent sticking. Grab one edge of the dough, stretch it up, and fold it over onto itself. Rotate the bowl 90° and repeat this up to 16 times, until the dough begins to tighten.
Gather the dough into a ball and flip it seam side down in the bowl.
Cover and let it rest for 15 minutes.
Repeat this process 5 more times (for a total of 6 sets), resting for 15 minutes between each set.

The dough being stretched and folded in a bowl.

The focaccia dough being stretched and folded in a bowl.

The stretched and folded dough being gathered into a ball and placed seam side down in a bowl.

5. Bulk Fermentation

Drizzle 2 tablespoons of olive oil into a clean bowl or straight-sided container.
Transfer the dough into the oiled container, making sure it’s lightly coated in oil to prevent sticking.
Cover and let the dough rise at room temperature until it doubles in size. This usually takes about 4 hours at 75°F or up to 12 hours at 65°F.

The dough in a straight-sided container with some olive oil before bulk fermentation.

The dough in a straight-sided container with some olive oil after bulk fermentation.

6. Transfer Dough to Pan

Line a 9"x13" baking pan with parchment paper and drizzle 2 tablespoons of olive oil on top.
Gently transfer the dough to the prepared pan.
Use your fingers to press and stretch the dough toward the edges. If it springs back, let it rest for 10 minutes and try again.

The dough stretched into a square aluminum pan lined with parchment paper and coated in olive oil.

7. Proof

Cover the pan and let the dough proof at room temperature for about 2 hours or until it doubles and looks noticeably puffy.
For a tangier flavor, refrigerate the dough overnight after spreading it in the pan. Then, let it come to room temperature and proof before baking.

The dough in a square pan after proofing.

8. Dimple the Dough + Add Toppings

About 20 minutes before baking, preheat your oven to 375°F and position a rack in the center.
Lightly oil your hands and use your fingertips to poke deep dimples all over the surface of the dough.
Drizzle the top with the remaining 2 tablespoons of olive oil and sprinkle with kosher salt and your favorite herbs.

The proofed dough after being indented and coated with oil, salt, and herbs.

9. Bake and Serve

Bake for 25-30 minutes, until the focaccia is golden brown on top.
Let the focaccia cool in the pan for 10 minutes before removing it. Slice and serve warm.

The baked whole wheat sourdough focaccia in an aluminum baking pan.

Sliced whole wheat sourdough focaccia on a cutting board. One piece of flipped over to show the crumb.

How to Store

Store cooled whole wheat sourdough focaccia in an airtight container at room temperature for up to 2 days.

For longer storage, transfer to a freezer-safe container and freeze for up to 3 months. Thaw at room temperature and reheat in the oven before serving.

Serving Suggestions

This whole wheat sourdough focaccia is perfect served warm with a drizzle of olive oil or dipped into my marinara sauce or pesto sauce. It also makes a hearty side for sourdough pasta and meatballs or spinach caprese salad.

Three pieces of whole wheat sourdough focaccia stacked on top of each other.

A cover of a recipe ebook with the title "Everyday Sourdough: 27 Sweet & Savory Sourdough Discard Recipes." There is an image of sourdough discard cinnamon rolls on the front. At the bottom, it reads "By Ashley Petrie of Everyday Homemade."

Grab a copy today!

Are you tired of watching your sourdough discard go to waste?

It’s time to turn excess discard into something delicious with my new ebook - Everyday Sourdough!

Inside, you’ll find 27 tried-and-true sourdough discard recipes that will transform your leftover starter into mouthwatering creations your family and friends will love.

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More Sourdough Recipes

📖 Recipe

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Whole Wheat Sourdough Focaccia

Course Bread

Cuisine Italian

Prep Time 1

Cook Time 30

Total Time 1 30

Servings pieces

Calories 160kcal

Author Ashley Petrie, RDN, LDN

Equipment

9"x13" aluminum baking pan (or an 18"x13" half sheet pan for thinner focaccia; or two 8"x8" aluminum baking pans), glass or ceramic may also be used
Kitchen scale
Mixing bowls
Bowl scraper
Straight-sided container (optional)

Ingredients

4 cups (480 grams) whole wheat flour
2 cups (480 grams) warm water 80-90℉
½ cup (100 grams) active sourdough starter or "fresh" discard less than one week old
4 ¼ teaspoons (12 grams) Diamond Crystal Kosher Salt measure by weight or use about half volume if using table salt or Morton's brand
6 tablespoons extra virgin olive oil divided
Additional kosher salt for sprinkling on top
Fresh or dried herbs for sprinkling on top

Instructions

Feed your sourdough starter 6-12 hours before starting the dough to make sure it’s bubbly and active. It will take around 6 hours if your kitchen is warm (75°F) or closer to 12 hours if it’s cooler (65-68°F).
In a large bowl, combine the whole wheat flour and warm water. Stir until no dry flour remains. Cover and let it rest for 1 hour (this step is called autolyse - it helps the dough hydrate and start building gluten).
4 cups (480 grams) whole wheat flour, 2 cups (480 grams) warm water
After the 1-hour autolyse, add your sourdough starter and salt to the bowl. Mix everything together by hand until a sticky, wet dough forms. Cover and let it rest for 15 minutes.
½ cup (100 grams) active sourdough starter, 4 ¼ teaspoons (12 grams) Diamond Crystal Kosher Salt
Wet your hand to prevent sticking. Grab one edge of the dough, stretch it up, and fold it over onto itself. Rotate the bowl 90° and repeat this up to 16 times, until the dough begins to tighten. Gather the dough into a ball and flip it seam side down in the bowl. Cover and let it rest for 15 minutes. Repeat this process 5 more times (for a total of 6 sets), resting for 15 minutes between each set.
Drizzle 2 tablespoons of olive oil into a clean bowl or straight-sided container. Transfer the dough into the oiled container, making sure it’s lightly coated in oil to prevent sticking. Cover and let the dough rise at room temperature until it doubles in size. This usually takes about 4 hours at 75°F or up to 12 hours at 65°F.
Line a 9"x13" baking pan with parchment paper and drizzle 2 tablespoons of olive oil on top. Gently transfer the dough to the prepared pan. Use your fingers to press and stretch the dough toward the edges. If it springs back, let it rest for 10 minutes and try again.
Cover the pan and let the dough proof at room temperature for about 2 hours or until it doubles and looks noticeably puffy. For a tangier flavor, refrigerate the dough overnight after spreading it in the pan. Then, let it come to room temperature and proof before baking.
About 20 minutes before baking, preheat your oven to 375°F and position a rack in the center.
Lightly oil your hands and use your fingertips to poke deep dimples all over the surface of the dough. This helps redistribute air bubbles and gives focaccia its signature look. Drizzle the top with the remaining 2 tablespoons of olive oil and sprinkle with kosher salt and your favorite herbs.
Bake for 25-30 minutes, until the focaccia is golden brown on top.
Let the focaccia cool in the pan for 10 minutes before removing it. Slice and serve warm. Enjoy!

Notes

Quick Tip: For best results, use a scale to measure ingredients by weight (grams).
Storage: Store cooled focaccia in an airtight container at room temperature for up to 2 days or freeze for up to 3 months.

Nutrition

Did you try this recipe?Let me know! Comment below, or take a picture and tag me on Instagram @everydayhomemadebyashley.