image of whole wheat pizza dough made with sourdough and freshly milled flour (whole grains)

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I got this recipe from a Mennonite friend who makes pizza every Saturday night using this basic pizza dough recipe.

Her pizza is incredibly delicious, and she bakes the crusts in multiple cast-iron pans to get crisp and chewy bottoms.

image of a healthy sourdough pizza dough made with fresh milled flour

After years of making pizza for my family, I will admit I have some high pizza standards. This easy pizza dough recipe, paired with homemade pizza sauce, makes an outstanding crust that is so flavorful and way better than the white flour pizza dough crusts!

image of a soft, thick and crusty sourdough pizza crust made with freshly milled flour

It’s healthier, way easier on my gut, and is so effortless to make! I mix the freshly milled flour with the sourdough starter, perform a few stretch and folds, then pop the dough in the fridge or stretch it out and top it with all the toppings. It doesn’t really need to rise after the initial bulk rise.

image of a very soft and supple pizza dough made with sourdough and whole wheat flour

This whole wheat pizza dough recipe is easy to make because it works with commercial yeast if sourdough isn’t your thing. All the other ingredients stay the same. And if you loathe stretch and folds, mix the dough in a stand mixer, then leave it alone. I prefer to mix it all by hand and do a few stretch and folds so, I don’t have to clean my mixer but either method is mostly hands off! Which is perfect for busy moms.

image of a whole wheat sourdough pizza slice zoomed in. Slice is topped with tomatoes, ranch dressing, mozzarella cheese, bacon bits, chicken, and red onion.

Sourdough Pizza Dough With Fresh Milled Flour: Ingredients & Substitutions

  • Fresh Milled Flour for pizza dough is best made from grains like hard white wheat or hard red. Spelt grain has less gluten than some modern wheat varieties, so use half-and-half to make pizza dough if you wish to use Ancient grains.
  • Very Active Sourdough Starter- I generally feed mine 4 hours prior to making pizza dough. If you are using commercial yeast than omit the starter and add 1-2 Tbsp of dry active yeast to the water. If you’re planning to refrigerate it, use 1 Tbsp and 2 Tbsp if you’re using it soon. Everything else stays the same. This is a hydrated dough that yields fluffly and chewy pizza crust.
  • Honey- maple syrup or organic cane sugar works in place of the honey.
  • Filtered water- I use well water and advise filtered water anytime you’re working with sourdough.
  • Olive Oil- when I run out of olive oil, I’ll usually use any neutral-flavored oil like avocado oil or sunflower oil (which are what I keep on hand).
  • Salt- like sea salt or Redmond are my favorites.
whole wheat sourdough pizza dough in the making
Whole wheat sourdough pizza dough is in the making with simple ingredients of sourdough, fresh milled flour, honey, water, olive oil, and salt.
  • Note: this pizza crust is vegan, so you can use dairy-free toppings to make a vegan pizza.

Toppings:

Our family’s toppings of choice are usually pepperoni and cheese. However, it also depends on what veggies need to be used up. Today, I made one crust with pesto sauce, mozzarella cheese, sliced tomatoes, red onions, roasted red peppers, and olives.

Sourdough pizza dough made with fresh milled flour and topped with homemade pesto, mozzarella, tomatoes, olives, roasted red bell peppers, and red onion.

The second pizza was with homemade ranch dressing, cheese, canned chicken, bacon bits, tomatoes, and red onion. Both were delicious!

Second pizza made with homemade ranch dressing, mozzarella, bacon bits, tomatoes, chicken pieces, and red onion.

Mise en PlaceEverything You Need!:

Homemade pizzas bake great on a pizza stone. However, you don’t need one to make delicious pizza. Preheating a baking sheet or cast-iron pan helps the bottoms crisp up. But honestly, I just crank up the oven to get pizzas that are nicely browned.

How To Make Whole Wheat Sourdough Pizza Dough (My Tips)

This is a really easy homemade pizza dough recipe! As I said, my friend makes this weekly, using white flour or yeast when needed. I’m sharing my best tips and tricks so that you can make it perfectly at home every time! Let’s walk through all the steps!

Note: You can make this sourdough pizza dough by hand or use a stand mixer fitted with the dough hook. If mixed by hand, you will need to do at least 4 stretch and folds to develop the gluten. Whereas using a mixer, you’d knead the dough for 20 minutes (this is a whole wheat crust, it needs a longer time to develop the gluten).

When your sourdough starter is bubbly and active, make the pizza dough and knead it in a mixer or make it by hand using my tips above. Give the dough 4-6 hours of resting time after the initial kneading.

If you are refrigerating the dough, make sure the gluten is fully developed by that time. So, either make your last stretch and fold, or make sure it’s fully kneaded in a mixer and passes the window pane test. I like to place the dough into a lightly greased Zip-lock bag, then refrigerate. The dough is ready to be used straight from the fridge. It’s very pliable and should have lots of air bubbles after it ferments!

Sometimes I let the dough hang out on the counter before storing it in the fridge; this also improves the softness and ferments a bit before slow fermentation in the fridge.

I like to use warm water or even room temperature water since the freshly milled flour is very warm straight from the grain mill. You want to get things going with sourdough, so don’t use cold water. Anywhere from 70-90°F is good. I wouldn’t do anything warmer with fresh milled flour.

Preheat the Oven

I have a pizza bake function on my induction oven that heats up to 480°F. Preheat the oven to 480°F or 500°F if you don’t have a convection oven. Get your pizza pans out and lightly grease them. I used an extra-large cast-iron and a round steel USA pizza pan. You can still make delicious and chewy pizza crust without preheating a stone or pan. Just make sure you get your oven very hot!

Make Pizza Sauce

I like to can big batches of pizza sauce using ripe tomatoes from the garden. However, this 5-minute sauce is fantastic, with canned tomatoes, if you like a savory tomato sauce made from scratch.

Make Healthy Sourdough Pizza Dough

Weigh your whole grains. I used 500 grams of hard white wheat berries. Or mill the grains and measure out 4 cups of freshly milled flour.

milling the wheat berries for sourdough whole wheat pizza dough

Ideally, your looking for a wheat berry that has higher protien inorder to bring the gluten out. Gluten is what makes the pizza dough pliable and stretchy. Less gluten, and the dough will tear.

When the sourdough starter is active and bubbly, add it to the water. Add in the olive oil, honey, freshly milled flour, and salt. Using your hands, mix everything well. The pizza dough will look shaggy and wet. Cover it with plastic wrap and come back to it in 20 minutes.

image of shaggy dough from the homemade whole wheat sourdough pizza dough

If you prefer not to get your hands dirty, simply combine the ingredients in the bowl of a stand mixer and knead it over low speed (speed 2) for 20 minutes or until it passes the window pane test. Then let it rise for 4 hours, covered.

After 20 minutes of mixing the dough by hand, perform the first stretch and fold. The dough will be more stretchable and pliable at this point, and with each time, the gluten will be developed. Do a total of four stretch and folds every 20 minutes. Then allow the dough to bulk rise for 4 hours.

image of sourdough pizza dough made with fresh milled flour. Performing a stretch and fold

After 4 hours of bulk fermentation, you can either place the dough ball into a greased Ziploc bag (I spray mine with avocado oil) and refrigerate it. Or divide the dough into two equal pieces and roll out to the desired pizza crust shape.

image of fluffy and risen whole wheat sourdough pizza dough
Pizza dough after bulk fermentation.

Optional-Letting it Rise

If you have extra time, you can let the pizza dough rise in the pans a bit. This can take 30-50 minutes. However, my pizzas usually rest as I’m preheating the oven and topping them. This amount of time (probably 10 or so minutes) still makes a deliciously soft, tender, and thicker crust, but it’s not required.

From-Scrtach Hacks

If you make a lot of homemade dough, this pizza roller will be so handy. I love that it works well with tackier dough and that you can use it in the pizza pan (not all do). Another must-have is a large pastry mat or piece of parchment paper to transfer your dough to a pizza stone or pan. I like to use oil and just shape my crust in the pan for minimal equipment.

Roll Out The Pizza Dough

Once the whole wheat pizza dough is fermented, smooth, and elastic, you’ll divide it in half (this recipe makes two medium-sized crusts). And form it into your desired shape.

I like to stretch my pizza dough into circular rounds because that is the shape of my pizza pans. Sometimes I’ll just roll out the entire dough ball onto an 18×13 sheet pan if I’m in a rush.

image of Alyona stretching out the whole wheat sourdough pizza dough in a cast-iron pan.

I like to grease my pizza pan well with olive oil and stretch each piece of dough directly into it.

If you’re avoiding excess oil than just flour a surface and roll out the pizza dough to about 1/2-inch thickness. Do this on parchment paper if you are transferring the dough onto a pizza stone.

Add the Sauce & Toppings

Once the dough is stretched and shaped to your desired thickness, slather on the sauce. Then add your desired toppings.

image of pesto pizza made with a healthy sourdough pizza dough made with 100% fresh milled flour

I like to add a thin layer of cheese, then add the toppings, and finish with another light layer of cheese. This makes it look like it came from a pizzeria!

If your feeling extra adventorus brush the crust with melted butter and sprinkle with some herbs and seasonings (like garlic powder, pizza seasoning, Italian seasoning, parmesan cheese, etc..)

Bake the Pizza

Once your wholesome pizzas are assembled, slide them straight into the preheated oven. Bake the pizza at a high oven temperature of 480°F for 15-18 minutes. The cheese should melt, and it should be speckled with brown spots on top. The crust should be golden brown.

image of whole wheat sourdough pizzas baking in the oven

Watch the pizza so it doesn’t brown too quickly. The last few minutes of baking can go from almost done to almost burnt, so be careful not to forget about it.

Serve

Remove the pizzas from the oven and place pizza pans on pot holders. Allow the pizzas to cool for 5-10 minutes. Then slice each pizza pie into 8 equal pieces. I like to use a sharp spatula to cut through any stubborn edges.

We cut our pizzas with a round pizza cutter, then trim any stubborn edges with a sharp spatula or bench scraper.

I love serving this healthy homemade pizza with a green lettuce salad, like Greek salad or Caesar’s salad.

To Make Ahead

I simply place my pizza dough into the fridge after bulk fermentation. Sometimes I’ll put it into the fridge after the fourth stretch and fold, and that works too. Using a zip-lock bag makes clean up so easy, as I can dispose of the bag afterwards.

Whole Wheat Sourdough Pizza Dough can keep in the fridge for up to 5 days. I like it best on day 2 or 3, but overnight or the day of still yields a delicious pizza crust.

How To Freeze Sourdough Pizza Dough:

There are a few different ways to freeze this pizza dough.

  1. Grease the inside of a Ziploc and form the dough into a ball. Place it into the Ziploc bag and remove as much air as possible (to prevent freezer burn).
  2. Prick the dough with a fork throughout the center. Par-bake the crust for 5-7 minutes without the toppings. Let it cool, then double wrap in plastic and freeze. You can add the toppings before baking.
  3. Pre-bake the crust as directed above, and only after cooling the crust, add the sauce and toppings. Flash freeze the pizzas, then double wrap each pizza and freeze inside Jumbo freezer bags. This makes great freezer meals for expecting moms! Double or triple the pizza dough to make plenty!

FAQs About Sourdough Pizza

Can I Use Yeast?

Yes! This pizza dough was adapted from a basic recipe that called for commercial yeast. Because this is freshly milled flour pizza dough, it could benefit from the starter’s extra hydration, so all the ingredients remain the same. Originally, the recipe called for 1-2 Tbsp of dry active yeast instead of the 1 cup of starter.

Can I Use White Flour?

Absolutely! This recipe was originally a white flour recipe that called for all-purpose or bread flour. Use 4 cups of white all-purpose flour or Einkorn flour.

Can I Freeze Sourdough Pizza Dough?

To freeze a pizza crust made with a sourdough starter, ensure it has completed the bulk fermentation process and that the gluten is fully developed. Freeze it whole in a greased gallon freezer bag.

Once frozen, let it sit in the fridge overnight to thaw. Take it out of the fridge two hours before shaping, and let it come to room temperature and rise a bit. Then shape into a crust and bake with desired toppings. You could let it rise in the pans for 30 or so minutes to ensure a fluffier crust.

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Whole Wheat Sourdough Pizza Dough Recipe

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This is the best wholesome pizza dough recipe ever–soft, chewy, and delicious! It's made with sourdough and 100% fresh milled flour. It's our family's favorite pizza crust, suitable for yeast or other flours. Bake it the same day or refrigerate it for easy weeknight suppers! It is the most supple, stretchy, and soft dough to work with. Simply stretch it out with your hands and forget the rolling pin!
image of a homemade, soft, sourdough pizza crust with fresh milled flour (made from whole grain wheat berries)
Prep Time: 1 hour 5 minutes
Resting Time: 4 hours
Total Time: 5 hours 5 minutes
Servings: 16 slices or 2 medium pizzas
Course: Main Dish
Cuisine: American

Equipment

Ingredients 

Sourdough Pizza Dough:

  • 1 1/2 cups warm water
  • 1 cup active sourdough starter
  • 2 Tbsp honey
  • 1/4 cup olive oil
  • 1 1/2 tsp salt
  • 4 cups whole wheat flour, (500 grams hard white wheat berries)

Instructions

  • Weigh 500 grams of hard white wheat berries and run them through a grain mill. You should have 4 cups of freshly milled flour.
    image of hard white wheat berries being milled in a grain mill to make whole wheat sourdough pizza dough
  • In a large bowl, mix together 1.5 cups of water, 1 cup of starter, 2 Tbsp of honey, 1/4 cup of olive oil, 1.5 tsp of salt, and 4 cups of the freshly milled flour. Dough will look shaggy and sticky. Cover it with plastic wrap and allow it to sit for 20 minutes. **See mixer instructions below.
    image of sourdough whole wheat pizza dough mixed in a bowl by hand (dough looks very sticky and shaggy at this stage)
  • After 20 minutes, do your first stretch and fold. Repeat this every 15 minutes for a total of four times.
    image of sourdough pizza dough made with fresh milled flour. Performing a stretch and fold
  • The dough will be very stretchy and elastic after the final stretch-and-fold. You can either refrigerate the dough in a greased bag or let it rest for 4 hours to bulk ferment.
    image of fluffy and risen whole wheat sourdough pizza dough
  • After bulk fermentation (or after rising 4 hours), divide the dough in half and shape it into the desired pizza shape. Top with your favorite pizza toppings and bake the pizzas for 15-18 minutes in a preheated 480°F oven. Enjoy!
    image of homemade sourdough whole wheat pizza dough being stretched out in a greased cast-iron pan

Notes

  • Pizza toppings shown: I made one crust with homemade pesto, mozzarella, tomatoes, roasted red peppers, black olives, and red onion. The 2nd pizza was topped with homemade ranch dressing, mozzarella, bacon bits, cooked chicken, tomatoes, and red onion. 
  • This crust can be used to make a Vegan crust. 
  • To make with commercial dry active yeast, use 1-2 Tbsp and mix it into the warm water. All the other ingredients remain the same.
  • To Make Dough in a stand mixer, combine all the dough ingredients and knead for 20-25 minutes, until it passes the windowpane test. Then bulk rise the dough for 4 hours. If you make pizza dough this way, you don’t need to do stretch and folds as you will develop the gluten from the kneading. Fresh milled flour doughs require longer kneading times than regular white flour doughs. 

Nutrition (per serving)

1slice Serving154kcal Calories27g Carbs4g Protein4g Fat1g Saturated Fat1g Polyunsaturated Fat3g Monounsaturated Fat220mg Sodium110mg Potassium3g Fiber2g Sugar3IU Vitamin A0.01mg Vitamin C11mg Calcium1mg Iron
Nutrition Facts
Whole Wheat Sourdough Pizza Dough Recipe
Serving Size
 
1 slice
Amount per Serving
Calories
154
% Daily Value*
Fat
 
4
g
6
%
Saturated Fat
 
1
g
6
%
Polyunsaturated Fat
 
1
g
Monounsaturated Fat
 
3
g
Sodium
 
220
mg
10
%
Potassium
 
110
mg
3
%
Carbohydrates
 
27
g
9
%
Fiber
 
3
g
13
%
Sugar
 
2
g
2
%
Protein
 
4
g
8
%
Vitamin A
 
3
IU
0
%
Vitamin C
 
0.01
mg
0
%
Calcium
 
11
mg
1
%
Iron
 
1
mg
6
%
* Percent Daily Values are based on a 2000 calorie diet.

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