Whole Wheat Pizza Crust

Baking with whole wheat can be tricky. When I first started, I quickly learned replacing whole wheat flour with white flour 1:1 won’t bring good results. I also realized there is a huge difference between whole wheat flour and whole wheat pastry flour. Whole wheat flour is generally ground from hard white wheat. It has a higher protein and gluten count so it’s best used for breads. Whole wheat pastry flour is ground from soft white wheat and has a lower protein and gluten count providing for a soft and tender crumb.

For years, I tried making whole wheat pizza crusts but always came up short. They were either too tough, too “wheaty”, or flat-out unpalatable. Then I discovered Peter Reinhart’s book Whole Grain Breads. What a life-saver this book is! He has a recipe for just about every kind of bread imaginable using all whole grain flours! His pizza crust is fantastic. The method he uses to prepare the dough makes it pliable, soft and easy to work with.

For this pizza I used three cheeses, garlic, slivered almonds, and topped it with lightly dressed arugula. A whole wheat pizza with salad on top – a whole meal in a bite.

Whole Wheat Pizza Dough

Serving Size: Makes 4 12-inch pizzas

Whole Wheat Pizza Dough

This recipe requires a little forethought, but don't be intimidated. The night before, you mix a few ingredients in two different bowls. The next day, you combine these two doughs and add a few more ingredients. Let the dough rise and you're ready.

Adapted from Peter Reinhart's Whole Grain Breads.

This recipe was posted before I began posting all grain-free recipes on my site. Click here for a grain-free pizza recipe.


  • 1 ¾ cups whole wheat flour (not pastry flour)

  • ½ teaspoon sea salt

  • ¾ cup plus 2 tablespoons water
  • Biga:
  • 1 ¾ cups whole wheat flour (not pastry flour)

  • ¼ teaspoon rapid-rise yeast

  • ¾ cup plus 2 T water
  • Final Dough:
  • Biga

  • Soaker

  • 7 Tablespoons whole wheat flour (not pastry flour)

  • 5/8 tablespoon salt

  • 1 ½ teaspoons rapid-rise yeast

  • 2 ¼ teaspoons honey, or 1 tablespoon sugar

  • 3 tablespoons olive oil

  • Extra whole wheat flour for adjustments
  • Toppings for Pizza shown above:
  • 6 tablespoons olive oil, divided

  • garlic powder
sea salt

  • 2 cups mozzarella, grated

  • 2 cups fontina, grated

  • 1 cup pecorino romano, grated

  • 1 cup slivered almonds

  • 4 cups arugula

  • 1 lemon


For Soaker:

Mix all the ingredients together in a medium bowl for about 1 minute. Cover and leave at room temperature overnight.

For Biga:

Mix all the biga ingredients together in a bowl until they form a ball of dough. Using wet hands, knead the dough for 2 minutes, the dough will feel very tacky. Let the dough rest for 5 minutes and then knead it again (with wet hands) for 1 minute. Place the dough in a clean bowl and cover tightly. Refrigerate overnight.

The next day - Remove the biga from the fridge 2 hours before mixing the final dough to take off the chill.

Place the biga on a floured surface. Pull the soaker out of its bowl and place it on top of the biga (you will stack the doughs on top of one another). Using a metal pastry scraper or knife, chop the doughs into 12 pieces. Place pieces in the bowl of a standing mixer (see below for instructions to mix by hand). Add the 7 tablespoons of whole wheat flour, salt, yeast, honey, and 2 tablespoons olive oil to the dough. Mix with the paddle attachment on slow speed for 1 minute. Switch to the dough hook and mix on medium-low speed for 2 minutes until the doughs become cohesive. Add more flour or water as needed until the dough is soft and slightly tacky.

To mix by hand:

Place the dough pieces in a large bowl. Add the 7 tablespoons of whole wheat flour, salt, yeast, honey and 2 tablespoons olive oil to the dough. Knead with wet hands for 2 minutes until all of the ingredients are incorporated. The dough should be soft and slightly tacky.

Dust a work surface with flour and roll the dough in the flour to coat. Knead the dough for 3-4 minutes, incorporating only as much flour as needed until the dough is soft and tacky. Let the dough rest for 5 minutes. Line a baking sheet with parchment paper and oil it with the remaining 1 tablespoon olive oil. Knead the dough again for 1 minute. Divide the dough into 4 pieces and form each piece into a tight ball. Roll the balls in the oil and cover pan loosely with plastic wrap or a clean dish cloth. Let dough rise for 1 hour.

Preheat the oven to 500ºF and adjust rack to middle position. Place one ball of dough on a floured work surface. Using a rolling-pin, roll out to a 12-inch diameter disk. Brush with 1 tablespoon olive oil and sprinkle with salt and garlic powder. Spread ½ cup mozzarella, ½ cup fontina, ¼ cup pecorino, and ¼ cup slivered almonds over pizza. Bake for 9 minutes, until cheese is bubbly and just golden. Repeat with remaining dough.

To serve:

Toss arugula with juice from ½ a lemon, 2 tablespoons olive oil, and a sprinkling of sea salt. (Taste and season with more salt or lemon juice if needed) Place salad on top of each pizza, cut and serve.

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  1. Thank you, Carrie! I have a pizza dough recipe that I absolutely love, and make in very large batches, but it is all white flour. I am thrilled that you are giving this to us!
    Also, I am a little giddy from ordering a grain mill yesterday. Please keep giving us these tips about using whole wheat flour. There is so much on the internet that it was just overwhelming for me, and your book/blog has been a big help.

    My husband thought I was actually ordering stalks of wheat. Like they cut it from the field. That was my belly laugh for the day.

    • Deliciously Organic

      I’m thrilled you bought a mill! You are going to love it. It’s so great to be able to grind any kind of flour whenever I need to.

      That’s hilarious that your husband thought they were stalks of wheat. One time I told a friend I needed to go “pick up my cow” (meaning my meat order at the farm) and she turned and said, “Now Carrie, please don’t tell me you are seriously going to raise a cow in your backyard!” :)

  2. I love making pizza at home and I always make a whole wheat crust, it is so much more flavorful than using white flour. I have one of Peter Reinhart’s books, but not his whole grain book, I’ll have to check it out and I look forward to trying this recipe.

  3. Jennifer

    Do you know if this dough recipe will freeze? I would love to double up and freeze to always have on hand. I know our grocery store freezes their “homemade” dough and wasn’t sure if you would just wrap and freeze. Very excited to try this recipe – looks delish!

    • Deliciously Organic

      I’ve never tried freezing it, but I do know that after the dough balls have been formed you can refrigerate the dough for up to 24 hours to slow the fermentation process. If you try freezing and thawing I’d love to her how it goes!

    • Deliciously Organic

      I would think you could 1/2 this recipe with no problem. After you for the dough into balls you can then place them in the fridge for up to 24 hours to slow the fermentation process. I have no idea if you can freeze the dough. If you give it a try, let me know!

  4. This pizza dough looks absolutely amazing! It looks nice and thin and crispy yet chewy and soft. Exactly what I’d been looking for. I have been making my own whole wheat pizza dough for a while now but still haven’t found the perfect combination. This one looks like a little more work, but looks like it is well worth it. I will be giving it a try very soon (as in probably this week-end!) Thanks for sharing!

  5. nancy

    Thanks so much for this recipe I’ll try it tomorrow with hungarian stone ground high altitude wheat (we are at about 4,500 ft above sea level). Also we are just two people and since I have never made pizza dough before wondered if I can keep the other 3 dough pieces for any length of time or should I cook the 3 left by themselves with nothing added and freeze? I am so grateful to you for this recipe – have looked quite a long time and most recipes all have a mix of white and wheat flour – I want to now start using just wheat flour so thanks again :)

  6. nancy

    Ok Carrie and ladies all herein :) I am so excited about this I have to return the favor by giving y’all a tip for planting tomatoes in the garden :) Remove 1/3rd of the plant’s leaves at the bottom so that when you plant it – you will plant it deeper up to where the remaining leaves are on the stem – this gives the plant a better survival chance and most times will give you more tomatoes as well :) The plant will concentrate more on growing roots instead of leaves at first then the top will grow. Hope this helps – Organics Rule :)

    • Deliciously Organic

      Whole wheat flour (also known as hard wheat) will be labeled “whole wheat flour”. Whole wheat pastry flour (aka soft wheat flour) will say “whole wheat pastry flour” on the label. I buy my own grain and mill it myself (very easy and saves me money), but the walmart brand should work just fine. I also like King Arthur flour or Trader Joe’s.

    • Deliciously Organic

      I would start with omitting the olive oil all together and adding water in it’s place (the oil is needed for moisture). I haven’t tested the recipe without the oil, but that’s where I’d start. (Or, could you reduce it to 1 tablespoon oil and then add 2 tablespoons water to reduce the fat for your diet needs? Just a thought.) If you try it, please let me know how it turns out!

  7. New to Pizza Dough

    I have a question – you say to remove the Biga for 2 hours – do you also remove the starter at the same time or leave it in the fridge until you are ready to combine/stack the two? Thanks

    • Deliciously Organic

      After reading your comment, I realized there is a very small error in the recipe. The starter is supposed to stay at room temperature overnight (not in the fridge). I made the edit. Thanks for pointing that out!

  8. Gianna

    I know this post is from a long time ago, but I just made this tonight and I just have to say it is hands down the BEST pizza dough I have ever made! I am definitely sticking with this recipe. It might be a bit more work and take more preparation, but it is absolutely worth it. Plus, the fact that it makes four doughs means making pizza dough less often. So delicious… thank you for sharing!

  9. Stacie

    Could you roughly convert “overnight” into hours for me?? I mistakenly told my son that we were making this pizza tonight, but forgot to put the ingredients together last night. Maybe if I am early enough, I may still have time to do it!

  10. Stacie

    Thanks so much for getting back to me so soon! Whipped them out and got the Biga in the fridge. I think it will turn out just fine:-). We will just be eating a little later than usual. Will let you know how the “eight hour” version turns out!

  11. Lauree

    This was great! Just made this for the first time last weekend when we had our friends Christmas party. I doubled the recipe and came up with 7 crusts (could have done 8 if I had tried hard enough). Everyone liked it even though there were 10 adults and 11 kids. We are making it again today. :)

    • Deliciously Organic

      I haven’t had much luck substituting white whole wheat for whole wheat flour. The white whole wheat has produced a much more dense crust. If you have a little whole wheat pastry flour you could try substituting about 1 cup of the ww flour for pastry flour to help lighten the dough a bit.

  12. shawn

    I was just wondering if you could use stone grond whole flour for this recipe? Also I was wondering if you have the weights for the flour in this recipe instead of just the volume, whether it be the stone ground or regular whole wheat or both?


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