Looking for a from-scratch dinner recipe with whole grains? Learn how to make the perfect Stromboli recipe using freshly milled flour.

How to Make Stromboli with Freshly Milled Grains: A Wholesome, Delicious Twist
If you are ready to find a wholesome addition to your weekly dinner menu, you have come to the right place! Today, we’re diving into how to make stromboli with freshly milled grains, turning this Italian-American classic into a wholesome, hearty, and utterly delicious meal. Whether you’re a busy mom looking for something exciting for dinner or a homemaker eager to experiment with your freshly milled flour, this recipe has your name on it.

So, what’s the big deal about using freshly milled grains? Well, let me tell you. Freshly milled flour isn’t just a trend—it’s a game-changer. You get all the nutrients often removed from regular white flour, plus the added flavor of whole grains. We’ll walk you through the process of making this scrumptious Stromboli recipe from scratch and hopefully encourage you to add it to your weekly dinner menu.
What is Stromboli, Anyway?
Before we dive into the dough, let’s clear up any confusion. Is it a pizza? Is it a calzone? No, it’s not quite either, but it’s a glorious combination of both! A stromboli recipe is a stuffed bread, often filled with cheese, meats, and veggies, then rolled into a tight log and baked to golden brown perfection. I use my whole wheat pizza crust recipe as the base for this great recipe. Think of Stromboli as pizza’s cooler, more portable cousin.

So, now that we’ve gotten the stromboli basics down, let’s start on how to make this delicious creation with freshly milled grains.
Tools for Stromboli Recipe:
- Grain Mill (I use and recommend the Komo Mill, but the Nutrimill is a more affordable option)
- Kitchen Scale (so handy with fresh-milled flour)
- Kneading Board
- Rolling Pin
- Dutch Whisk (makes mixing a breeze)
Ingredients You’ll Need:
- Whole wheat flour (freshly milled is best, but store-bought works too)
- Warm water (about 110°F)
- Instant Yeast
- Olive oil (for a golden crust)
- Salt
- Marinara for dipping(a simple, tangy tomato sauce)
- Your Favorite Pizza toppings:
- Shredded mozzarella cheese
- Parmesan cheese
- Meats like pepperoni, sausage, or prosciutto
- Fresh veggies like bell peppers, spinach, or onions (you can make a veggie stromboli)
- Garlic Butter: Melted Butter, minced garlic and fresh parsley (you can also use garlic powder and dried parsley)
- Egg wash (to get that gorgeous golden color)
- Plastic wrap and parchment paper

Step-by-Step Guide to Making From-Scratch Stromboli recipe with Whole Wheat Flour
Now, let’s get down to business. Making this stromboli recipe from scratch is a bit of a labor of love, but trust me, it’s so worth it.
1. Prepare the Dough:
For the dough we are using my whole wheat pizza dough recipe. Start by placing your whole wheat flour and other dry ingredients into a large mixing bowl. If you’re using freshly milled flour, that’s even better—your dough will have an incredible texture and flavor. Create a well in the center of the large bowl and add in your wet ingredients, water and olive oil.

Use a wooden spoon, danish whisk or your hands to combine the wet and dry ingredients. Knead with your hands until there is no dry flour and the dough forms a cohesive ball.
2. Stretch and Fold, Stretch and Fold:
Stretch and folds are like lazy kneading with breaks in between. The purpose of kneading it is to encourage gluten development and good structure in our dough. So, we are going to do five sets of stretch and folds every 5 minutes. Each time you will notice your dough becoming more cohesive and stretchy. If it’s too sticky, add a little more whole wheat flour; if it’s too dry, splash in a bit more water. (See video for demonstration of stretch and folds.)
3. Give it a rest:
Overnight fermentation may feel like a hassle, but it is so worth it. This is probably the best baking hack I have learned from owning a bakery. Overnight fermentation results in an increase in flavor and a strong gluten network when paired with a series of stretch and folds. This is extra important with freshly milled whole grains because whole wheat flour absorbs liquid more slowly than all-purpose flour. This overnight rest gives the whole grain flour enough time to properly absorb all the ingredients. A little prep now results in an easy and quick meal later!
We keep our homemade dough in the fridge overnight so that the dough ferments slowly for the best flavor development. You want to remove your dough ball from the fridge about an hour before you plan to make your Stromboli so that the dough can reach room temperature before you try to roll it out.
A quick note about fermentation and whole wheat flour: Because freshly milled grains have so many nutrients that all-purpose flour does not, fermentation happens a lot faster. I can leave pizza dough made with all-purpose flour in the fridge for up to 5 days and it is still good. Pizza dough made from freshly milled whole grains would just be too sour at that point, so I try to use my dough within two days, optimally.
5. Roll Out the Dough:
Preheat your oven to 400°F (200°C). Divide your dough into two sections. Take one dough ball and turn it onto a lightly floured surface. Using a rolling pin, roll out the soft dough into a rectangle. Your goal is to get to a 10 in by 16 in rectangle. If your dough becomes difficult to roll, let the dough rest for about five to ten minutes and return to rolling. It should be much easier when given time to relax.

6. Add Your Fillings:
Start by spreading the garlic butter in a thin layer on the entire roll out. This gives the homemade pizza dough more flavor. Then, coat the edges of the rectangle in egg wash to seal up the stromboli and keep the fillings from escaping when baking.
Next, sprinkle with shredded mozzarella cheese. After the cheese layer add meats and veggies– pepperoni, spinach, mushrooms, green pepper, etc. I like to add some parmesan cheese and then top it all off with more mozzarella. I do not add any pizza sauce to my stromboli. Instead, I provide marinara on the side for dipping.
7. Roll and Seal:
Carefully roll the dough into a tight log, slightly pulling in the sides of the dough like you’re wrapping a burrito, ensuring the ends are sealed well so nothing spills out. Pinch the end of the roll like you’re making cinnamon rolls to make sure there is no spillage. Then, using a pastry brush, brush the top with an egg wash so that it turns a beautiful golden brown when it bakes. Using a sharp knife, cut 3-5 slits on the top of your roll. This will allow the steam to escape from your stromboli without busting out the sides.

8. Bake the Stromboli:
Place your stromboli on a baking sheet lined with parchment paper and bake for 25 minutes or until the crust is golden brown and the cheese inside is bubbling. Keep an eye on it—this part is where the magic happens.

9. Slice and Serve:
Once it’s out of the oven, let it cool for a few minutes. Then, use a sharp knife to slice it into thick, hearty slices. Serve with a side of marinara sauce for dipping.
FAQs About Making Stromboli with Freshly Milled Grains

Can I use whole wheat flour instead of plain flour?Absolutely! Whole wheat flour brings a heartier, nuttier flavor and is packed with nutrients. It may change the texture of the dough slightly, but it adds a wholesome twist to your stromboli recipe.
Can I use whole wheat flour instead of all-purpose for pizza? Yes, you can! Whole wheat flour will give your pizza or stromboli a heartier texture. However, by having an overnight fermentation paired with a series of stretch and folds, your pizza/ Stromboli dough will have a great texture and flavor.
How does whole wheat flour affect pizza dough? Whole wheat flour can make the dough heartier and less airy than all-purpose flour. However, we have curated this recipe specially for whole grains:) If you’d like to adjust to whole grains more slowly, you can always make this recipe using half whole grain and half all-purpose flour.
Does whole wheat flour rise with yeast? Yes! Whole wheat flour will rise with yeast, but it might take a little longer compared to refined white flour. Be patient and give your dough time..
Should stromboli have sauce inside?
I prefer to keep it on the side for dipping because it allows the dough to bake better on the inside. This stromboli recipe is baked at a high temperature, allowing it to get a nice crispy outer layer, as well as a well baked inner layer (no raw dough here!). A big part of that is that there is not a lot of liquid inside this recipe. Besides, dipping is so fun!
Conclusion: Why You Should Try This Whole Wheat Stromboli Recipe
Making stromboli with freshly milled grains isn’t just a fun cooking project—it’s a great way to incorporate more wholesome, nutritious ingredients into your meals. By using whole wheat flour, you’re not just making your stromboli taste better; you’re packing it with fiber, protein, and essential nutrients. Plus, the process of milling your own flour can be a rewarding and sustainable way to enjoy bread-making.

So, whether you’re making it for dinner tonight or trying it out over the weekend, this recipe is sure to be a hit with your family. Don’t forget to share your results with us—we’d love to see your stromboli creations!

Stromboli Recipe with Freshly Milled Flour
Ingredients
Dough
- 595 grams 4 2/3 cups whole wheat flour
- 12 grams 2 teaspoons salt
- 3 grams 1 teaspoon instant yeast
- 405 grams 14.25 oz water, room temperature
- 28 grams 1 oz extra virgin olive oil
Garlic Butter
- 3 Tb butter
- 2 tsp minced garlic
- 2 tsp fresh parsley
Filling
- 3 cups mozzarella
- 1/2 cup parmesan cheese grated
- 1 pound pepperoni
Marinara
- 1 Quart crushed tomatoes
- 1 tsp basil
- 1 tsp oregano
- 1 tsp dried parsley
- 1 tsp salt
- 1 Tb sugar optional
Egg Wash
- 1 large egg beaten
- 1 tbsp water
Instructions
- Mill your wheat berries into flour using the finest setting on your grain mill.
- In a large bowl, combine your freshly milled flour with salt and yeast. Whisk together to distribute evenly.
- Add water and olive oil. Mix until no dry flour remains. The dough will be slightly sticky – this is normal with fresh-milled flour.
- Cover and let rest for 30 minutes. This crucial autolyse period allows the fresh flour to fully hydrate.
- Perform five sets of stretch and folds at 5-minute intervals, keeping the dough covered between sets.
- Place dough in the refrigerator, in an airtight container, overnight and up to 48 hours.
- The day you want to bake the pizza, remove dough from refrigerator at least an hour before you plan to bake it to allow it to come to room temperature.
- Divide dough into two sections and roll each section out into a 10 in by 16 in rectangle.
- Apply thin layer of garlic butter and then use a pastry brush to brush egg wash on the edges of your rectangle.
- Apply a layer of cheese, then a layer meat and then finish with a final layer of cheese.
- Roll your rollout towards you tucking in the sides like a burrito. Roll untill you reach the other side and then pinch the end of the roll out to the log (watch video).
- Egg wash entire top of stromboli and cut 3-5 slits in the top of the roll to allow steam to escape while baking.
- Bake at 400 degrees F for 25 minutes or until the bottom is brown and the top is golden.
- To make marinara add crushed tomatoes and all spices to a saucepan and bring to a simmer. Remove from heat and serve.
- Cut into strips and serve with a side of warm marinara
Video
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