Easy Whole Wheat Pizza Dough with freshly milled flour! This Whole Wheat pizza crust is so quick to make using hard white wheat (grain) that you mill at home. It’s so easy to make whole wheat flour if you have a grain mill! It yields a soft chewy crust and freezes great when you need frozen pizza in the oven for a fast dinner! You will love this sausage and pepperoni pizza made completely from scratch (including the quick pizza sauce)!

whole wheat pizza dough with freshly milled flour

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Whole Wheat Bread and Pancakes have become a staple using freshly milled flour! Making Whole Wheat pizza dough is just as easy as making your favorite homemade pizza dough recipe! Matter of fact, this pizza dough crust was actually converted from a white flour recipe!

Whole Wheat Pizza Dough for Beginners:

If you’re new to the freshly milled flour journey, this is a no-fuss recipe for beginners. All you need is 5 basic ingredients, hard white wheat, and a grain mill. I keep all of my basic grains and mill on the counter so I can quickly walk up to my baking corner and make the whole wheat flour, it takes seconds to mill and dump everything into a stand mixer to finish the dough. Basically, it’s mostly hands-off!

pizza from freshly milled flour

This pizza crust recipe comes from a friend. It was originally with white flour which I converted to a 100% whole wheat pizza dough recipe. Yes, you can use freshly milled whole wheat flour for pizza dough that the kids will even eat! My son requested this pizza later the same evening and the next day too! So, let’s just say it’s a win-win if kids love it!

fluffy and chewy pizza dough made from freshly milled flour

Homemade Whole Wheat Pizza Dough Ingredients:

This recipe for whole wheat pizza dough comes together with simple ingredients. If all you have is all-purpose or bread flour, you can simply use 2 cups of that. This makes a deliciously thick and soft crust with a crisp bottom!

  • Yeast- I typically use dry active yeast but you can use instant yeast too.
  • Water- use warm water to hasten the rise time. I like my water to be anywhere from 80-100°F. Anything higher than 130°F can kill the yeast.
  • Whole wheat flour- in pizza dough should be mostly a hard wheat variety like hard white wheat or hard red. Mix in a small amount of kamut for variation. I like to use hard white wheat as it’s very mild for whole wheat flour. It’s also known as white whole wheat flour. Whole wheat pastry flour is low in gluten but even that seemed to work for someone with this kneading method.
  • Oil- I like to use extra virgin olive oil.
  • Salt- use a natural sea salt.
  • Honey- is a healthy sweetener that works great for this pizza dough.
  • Cornmeal- isn’t used in the dough but used

To Make Sourdough Whole Wheat Pizza Dough: omit the yeast and add 1/2 cup of active sourdough starter. Also, decrease the water to 2/3 cup.

How To Make Whole Wheat Pizza Dough:

Pizza dough with whole wheat can be more tricky to work with than white flour. The key is to knead longer so the freshly milled flour has time to absorb the liquid and develop gluten. It’s best to use a mixer with a hook attachment since the dough will appear to be very sticky, however, the longer it kneads the stretchier and pliable it will get. Use a bread machine and knead it in two dough cycles for the same results.

  1. Make the dough: proof the yeast in water, honey, olive oil, and salt for 5 minutes before adding the flour. This ensures the yeast is active if it blooms.
  2. Knead in a stand mixer on low for 25 minutes. I like to knead on speed number 2 in my Kitchen aid mixer. This long kneading method is something I learned from the Grains In Small Places blog, it works amazingly with freshly milled flour recipes!
  3. Rise: place the dough in a greased bowl and let it rise for one hour. Cover the dough with a kitchen towel or plastic wrap so it doesn’t dry out.
  4. Shape the dough into one large pizza crust or make 2 medium thin-crust pizzas. If making one large crust roll dough out into a 16-inch circle. Dust cornmeal on the surface before rolling it out so the dough doesn’t stick to the surface.
  5. Top with pizza sauce, cheese, and toppings like pepperoni and sausage.
  6. Bake in a preheated 450°F oven for 10 minutes (I bake mine on the bottom rack of the oven for a crisp crust).
  7. Cut into wedges and serve. Our favorite is Cheddar, Sausage, and Pepperoni Pizza!

Favorite Pizza Pans

I own a few different pizza pans and love this pizza screen for a super crisp bottom (dust dough well with cornmeal when using). However, for this pizza dough, I used my large Wilton 16-inch pizza pan for this crust since I was baking one large crust. To make thinner pizza use two 12-inch pizza pans.


Can I Make Ahead of Time and Freeze?

It is very easy to prepare the pizza dough and refrigerate it until needed. Pizza dough stores well in the fridge for 1-3 days. If you are not planning to use up the pizza dough in that time frame then it’s best to freeze the dough balls for up to one month. Another way to make this ahead is to par-bake the crust, top the cooled crust with your favorite toppings, and flash freeze. Once frozen double wrap in plastic wrap and use like you would frozen pizza (this is perfect for freezer meals).

How Do I Freeze Pizza Dough With Whole Wheat Flour?

You can make frozen whole wheat pizza from scratch and don’t ever need to buy frozen pizza again! Simply pre-bake the crust before you put on the toppings. Cool the parbaked crust and then top with pizza sauce, cheese, and any additional freezer-friendly toppings. Flash freeze until solid then double wrap in plastic wrap and freeze for up to 3 months. You will love this freezer-friendly meal!

To Bake Frozen pizza: preheat the oven to 400°F. Place frozen pizza on a pizza pan (or directly on the oven rack for a crispier crust) and bake for 15-18 minutes.

Favorite Sausage and Pepperoni Pizza:

This is one of the best whole-wheat pizza dough recipes! It’s made with a sweet and savory tomato sauce made from scratch, mild cheddar cheese, pepperoni, and breakfast sausage! I fell in love with the flavors when a lady brought this to church. The original recipe was with homemade pizza dough using white flour which I converted to using freshly milled whole wheat flour. The toppings are incredible for homemade pizza, almost like a meat-lover pizza only without the bacon!

whole wheat pizza dough from freshly milled flour

  • Top pizza crust with 1/3 cup of pizza sauce, 8 oz shredded cheddar cheese, 3/4 pound of pork sausage (or Jimmy Dean’s breakfast sausage), and 4 oz pepperoni. You can divide the cheese up and top half of it over the sausage.
  • For the quick pizza sauce: I mixed 1/2 cup of tomato paste with 1 tablespoon of olive oil and sugar, 1 tsp salt, 1/4 tsp garlic powder, and a couple of dashes of paprika, chili powder, cayenne pepper, oregano, and Italian seasoning.

Tips For Crispy Whole Wheat Pizza Dough: pre-bake the crust at 400°F for 5-7 minutes then top with toppings and bake another 10 minutes. You could also bake the crust on a pizza screen or pizza pan on the bottom rack of a 450°F oven. Use cornmeal or flour to stretch the pizza dough out. If you’re not using a pizza screen you can lightly grease a pizza pan for extra crispiness.

crispy whole wheat pizza dough

Whole Wheat Pizza Dough with Freshly Milled Flour

Prep Time: 30 minutes
Cook Time: 20 minutes
Rising Time:: 1 hour
Total Time: 1 hour 50 minutes
Servings: 8 large slices
Easy Whole Wheat Pizza Dough with freshly milled flour! This Whole Wheat pizza crust is so quick to make using hard white grain that you mill at home to make whole wheat flour! It yields a soft chewy crust and freezes great when you need frozen pizza in the oven for a fast dinner!



Pizza Dough:

  • 1 cup warm water
  • 1 Tbsp dry active yeast
  • 1 Tbsp honey
  • 2 Tbsp olive oil
  • 1 1/2 tsp sea salt
  • 325 grams hard white wheat (about 2 1/2 cups of freshly milled flour)

Sausage and Pepperoni Pizza:

  • 8 oz mild cheddar cheese (shredded)
  • 2 cups browned sausage (pork or breakfast sausage)
  • 4 oz pepperoni

Quick Pizza Sauce:

  • 6 oz tomato paste
  • 1 Tbsp olive oil
  • 1 Tbsp sugar
  • 1 tsp salt
  • 1/4 tsp garlic powder
  • 1/4 tsp paprika
  • 1/4 tsp chili powder
  • 1/4 tsp oregano
  • 1/16 tsp cayenne pepper
  • 1/2 tsp Italian seasoning
  • 1/4 cup water



  • freshly milled flour
    Weigh the grain and mill into flour.
  • proofed yeast
    In the bowl of a stand mixer whisk together the warm water, yeast, honey, olive oil, and salt. Allow the yeast to bloom for 5 minutes.
  • pizza dough with freshly milled flour
    Add the flour and knead over low speed for 25 minutes. I kneaded it on Speed 2 in my Kitchen-Aid mixer. The dough will be sticky. Rest for 1 hour covered in a greased bowl.
  • Meanwhile, combine the pizza sauce ingredients. I had to reheat my frozen tomato paste so I warmed it in a saucepan but you can mix everything together in a bowl.
  • rolled out pizza dough from freshly milled flour
    Preheat the oven to 450°F. Transfer the dough to a cornmeal-dusted surface and roll the dough out to a 16-inch circle. Transfer to a lightly greased pizza pan
  • Top the crust with all the pizza sauce, cheese, pepperoni, and sausage. Bake for 10 minutes on the bottom rack of the oven. Slice and serve.


  • This pizza dough recipe makes one extra large crust. 
  • Freshly milled flour weighs the same as the grain in whole form. So if you need 325 grams of flour simply weigh out the grains and that is how much flour you will need after it's milled. 
  • My quick pizza sauce recipe makes 2/3 cup of tomato sauce. This is enough for a large 16-inch pizza or two smaller pizza crusts. 

Nutrition per serving

Serving: 1large sliceCalories: 499kcalCarbohydrates: 33gProtein: 22gFat: 32gSaturated Fat: 12gPolyunsaturated Fat: 3gMonounsaturated Fat: 13gTrans Fat: 0.3gCholesterol: 73mgSodium: 1191mgPotassium: 365mgFiber: 5gSugar: 3gVitamin A: 386IUVitamin C: 1mgCalcium: 224mgIron: 2mg

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