Whole wheat pizza dough with freshly milled flour produces a hearty and delicious pizza crust perfect for all of your favorite toppings.

A pepperoni pizza on a wooden cutting board with one slice cut out.

Freshly milled flour adds extra flavor and a chewy, delicious texture to homemade pizza dough. With a handful of simple ingredients and one hour of rise time, you’ll have the perfect base for homemade pizza sauce, crumbled ground beef sausage or sliced pepperoni, and lots of cheese and veggies. 

Whole grains also give your pizza a boost of fiber, vitamins, and minerals. Store-bought white flour lacks the bran and germ, components of whole wheat that contribute to higher nutritional value. Milling your own flour keeps the nutrition intact, making pizza night that much more special.

One of our favorite ways to enjoy both freshly milled flour and delicious pizzas, this easy recipe makes four 12-inch pizzas that will easily feed the whole family. 

Choose traditional pizza toppings like pepperoni and sausage, or branch out with alfredo pizza or breakfast pizza toppings. Serve with a green salad, some pickled red onions, and a side of homemade ranch dressing for dipping. 

Why You’ll Love This Recipe   

Deep flavor – Freshly milled whole wheat adds robust flavor to homemade pizzas. It’s earthy and wholesome with a touch of natural sweetness.

Better nutrition – When milled fresh and used shortly after, wheat flour maintains more of its vitamins, minerals, and fiber than the flour you’d buy at the grocery store.

Great use of milled flour – If you’re new to milling flour, this whole wheat pizza dough recipe is a great avenue to put all your fresh flour to good use.

Ingredients

Ingredients in bowls on a white counter top.

Flour – I use soft white wheat berries, milled at home. Weighing freshly milled flour with a kitchen scale provides the most accuracy.

Water – I always recommend filtered water, and I love my Boroux filters.

Oil – Extra-virgin olive oil adds wonderful flavor, but you can use whichever oil you prefer.

Yeast – Instant yeast works more quickly, while active dry yeast has a slow rise. Try my sourdough pizza dough, too.

A full ingredient list with exact amounts can be found in the recipe card below.

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Tools You May Need

Grain mill – I use a Mockmill.

Stand mixer – A stand mixer makes the kneading process a breeze.

How to Make Homemade Whole Wheat Pizza Dough

A dough ball in a stand mixer bowl.

Step 1: Add flour, water, salt, oil, yeast, and sugar to the bowl of your stand mixer with a dough hook attachment. Mix on low to combine, then increase to medium speed and mix until the dough is smooth and elastic. Freshly milled flour requires longer kneading to develop the gluten. The mixing may take 8 to10 minutes or more. Use the windowpane test (see notes) to ensure the dough is ready. 

A dough ball doubled in size in a stand mixer bowl after the first rise.

Step 2: Once the dough passes the windowpane test, cover the bowl with a lid or a clean kitchen towel and let it rise for about one hour or until doubled. 

Four small dough balls on a countertop next to a plate of pizza toppings.

Step 3: While the pizza dough rises, preheat the oven to 425 degrees Fahrenheit. If using pizza stones, you can place them in the oven to preheat now. After the dough has doubled, place it on a lightly floured work surface and use a bench scraper to split it evenly into four pieces. 

Pizza dough rolled out on a white countertop with a rolling pin on top of the dough and bowls of pizza toppings on the side.

Step 4: Use a rolling pin to roll each of the four balls of dough into a 12-inch circle. Add sauce and your toppings of choice. 

Pizza toppings added to a pizza dough on a pizza pan.

Step 5: Place the pizzas on pizza pans and bake for 12 to 15 minutes or until cooked through and bubbly. The crust should be golden brown.

A half pizza on a pizza pan.

Step 6: Let the pizzas cool for several minutes before slicing. This lets the cheese set so that it doesn’t pull away from the crust during slicing. Enjoy!

Tips

  • Using warm water when mixing the dough may bring a faster rise.
  • If your dough is sticky, try wetting your hands or rolling it out between sheets of parchment paper. Adding more flour to the dough may result in a dry crust. Whole wheat flour is more absorbent than white flour, but it absorbs more slowly.
  • Rising dough in a warm place can speed up the process.
  • Placing the dough on parchment paper makes it easier to transfer to the pizza pans from your workspace.
  • A pizza stone preheated in the oven can produce a crisp crust.
  • Don’t overload the sauce or toppings. Too much on top can create a soggy crust.
  • If you are using freshly milled grains for this recipe, I recommend weighing the flour instead of using volume measurements. Grain mills vary greatly – some create very fine and fluffy flour, while others are a little more coarse. This makes volume measurements unpredictable. Using a kitchen scale and calculating the grams is much more reliable, ensuring you end up with a delicious end product. 
Three different pizzas next to each other on a counter top.

Recipe FAQs

How do I store homemade pizza?

Leftovers can be kept in an airtight container in the refrigerator. Homemade pizza also freezes well and can be reheated in the oven at a later time.

What does whole wheat pizza dough taste like?

A whole wheat pizza crust tastes wholesome and sweet, with a robust, earthy flavor. The chewy texture is enjoyable, though more dense than crusts made with all-purpose flour.

Can I make this dough ahead of time?

You can prepare the dough, wrap it in plastic wrap, and keep it in the refrigerator for a few days until ready to bake. Let it warm to room temperature before rolling out.

Does this dough freeze well?

When wrapped securely, this dough can be frozen for several months. Frozen pizza dough should be thawed in the refrigerator or at room temperature.

What pizza toppings go well with a whole wheat pizza crust?

Traditional toppings work just as well with a whole wheat crust as with a typical all-purpose flour crust. 

More Freshly Milled Recipes from the Farmhouse

If you try this recipe and love it, I would love it if you could come back and give it 5 stars! Tag me on Instagram @farmhouseonboone.

Whole Wheat Pizza Dough with Freshly Milled Flour

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Whole wheat pizza dough with freshly milled flour produces a hearty and delicious pizza crust perfect for all of your favorite toppings.
Prep: 20 minutes
Cook: 15 minutes
Additional Time: 1 hour
Total: 1 hour 35 minutes
Servings: 4 pizza crusts
Three different pizzas next to each other on a counter top.
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Ingredients

  • 4 cups soft white whole wheat flour, 560 grams
  • cups water, 354 grams
  • 2 teaspoons salt, 10 grams
  • 4 tablespoons olive oil, 44 grams
  • teaspoons yeast, 14 grams
  • 2 tablespoons sugar, 24 grams

Instructions 

  • Add flour, water, salt, oil, yeast, and sugar to the bowl of your stand mixer with a dough hook attachment. Mix on low to combine, then increase to medium speed and mix until the dough is smooth and elastic. Freshly milled flour requires longer kneading to develop the gluten. The mixing may take 8 to 10 minutes or more. Use the windowpane test (see notes) to ensure the dough is ready.
  • Once the dough passes the windowpane test, cover the bowl with a lid or a clean kitchen towel and let the dough rest for about one hour or until doubled.
  • Preheat the oven to 425 degrees Fahrenheit. If using pizza stones, you can place them in the oven to preheat now. After the dough has doubled, use a bench scraper and split it evenly into four pieces.
  • Use a rolling pin to roll the four balls of dough into circles about 12 inches wide. Add sauce and your toppings of choice.
  • Place the pizzas on pizza pans and bake for 12 to15 minutes or until cooked through and bubbly. The crust should be golden brown.
  • Let the pizzas cool for several minutes before slicing. This lets the cheese set so that it doesn’t pull away from the crust during slicing. Enjoy!

Notes

To perform the windowpane test, stretch a small amount of dough between your fingers. If it will stretch thin enough to see through without breaking, the gluten is developed enough. If the dough breaks while stretching, it requires more kneading to form the gluten strands.
If your dough is sticky, try wetting your hands or rolling it out between sheets of parchment paper. Adding more flour to the dough may result in a dry crust. Whole wheat flour is more absorbent than white flour, but it absorbs more slowly.
Rising dough in a warm place can speed up the process.
Placing the dough on parchment paper makes it easier to transfer to the pizza pans from your workspace.
Don’t overload the sauce or toppings. Too much on top can create a soggy crust.
If you are using freshly milled grains for this recipe, I recommend weighing the flour instead of using volume measurements. Grain mills vary greatly – some create very fine and fluffy flour, while others are a little more coarse. This makes volume measurements unpredictable. Using a kitchen scale and calculating the grams is much more reliable, ensuring you end up with a delicious end product. 

Nutrition

Serving: 1Pizza crust | Calories: 566kcal | Carbohydrates: 94g | Protein: 17g | Fat: 17g | Saturated Fat: 2g | Polyunsaturated Fat: 3g | Monounsaturated Fat: 11g | Sodium: 1172mg | Potassium: 470mg | Fiber: 14g | Sugar: 6g | Vitamin A: 11IU | Vitamin C: 0.01mg | Calcium: 45mg | Iron: 4mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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