Name: Best Whole Grain Tortillas
Prep time: 15 min
Cook time: 20 min
Total time: 30 min
Yield: 12
Ingredients: 3 cups (375 grams) freshly milled whole wheat flour (preferably hard white or red wheat); 1 teaspoon fine sea salt (5g); 1/4 cup (60 grams) avocado or olive oil; 1 cup (240 grams) warm water or milk; 1½ tablespoons vinegar (23g); ½ teaspoon baking soda

The best whole grain tortillas made from freshly milled flour are an easy, wholesome way to bring homemade goodness to your everyday meals. These whole grain tortillas are soft, flexible, and full of real flavor—all with simple ingredients!

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Homemade tortillas on a white plate with flour and wheat stalks beside

These homemade whole grain tortillas use just four pantry staple ingredients and come together quickly. They’re perfect for everything from wraps to quesadillas and tacos. And these homemade tortillas are better than even the best healthy store-bought tortillas!

There’s something special about baking with grains you’ve milled yourself. The flour is full of life—light, fragrant, and packed with nutrients that start to degrade within hours of grinding. If you’re wanting more whole foods in your diet, freshly milled wheat is a good choice. It is full of vitamins and is a good source of fiber. Plus, it makes the best tortillas!

I’ve did a taste test with both hard white and hard red wheat, and it works beautifully with either. The dough is forgiving and easy to roll out, and with a bit of rest, the tortillas cook up tender and pliable with those irresistible golden bubbles. Whether this is your first time baking with whole grains or you’re a long-time home miller, this recipe is one to keep on rotation.

We love to pair these whole grain tortillas with melted cheese and our favorite dried bean chili, white turkey or chicken chili, savory sweet potato chili, or smoky chipotle chicken soup.

If you’re already milling your own wheat, try our favorite sourdough with freshly milled flour or hearty whole wheat focaccia. If you need a little more help with alternative flours, the guide to baking with freshly milled flour can help, too!

Whole grain tortillas on a wooden cutting board

Why You’ll Love This Recipe

Easy to make: This whole wheat flour tortilla recipe doesn’t need yeast and has no long rising time. You’ll have warm tortillas in under an hour.

Truly whole grain: Unlike many “whole wheat” healthy tortillas at grocery stores, these homemade whole wheat tortillas are a better choice with 100% whole grain. Made from flour you just milled, they are higher in dietary fiber and have a lower glycemic index (don’t spike blood sugar as much) compared to white tortillas.

Flexible and freezer-friendly: These store beautifully in the fridge or freezer, and they’re sturdy enough for wraps but soft enough for tacos.

What Are Best Whole Grain Tortillas?

Whole grain tortillas are flatbreads made from 100% whole wheat flour, water, oil, and salt. Unlike white flour tortillas, whole-grain tortillas retain all the bran and germ from the wheat, giving them a nutty flavor and a more rustic texture. When made with freshly milled flour, the taste is far superior to store-bought or those made with pre-ground whole-wheat flour. A whole grain tortilla is a healthy tortilla option!

They’re not as puffy as naan or pita and don’t require yeast or sourdough starter. They’re closer to traditional corn tortillas but with the added flavor and nutrition of whole grain. This recipe makes them soft and rollable—no cracking or tearing, which is key for wraps and burritos.

Best Whole Grain Tortillas Ingredients

Freshly milled whole wheat flour: I love using hard white wheat for a milder flavor and the best whole wheat tortillas. You can also use hard red for a heartier taste.
Warm water: Helps hydrate the bran and develop elasticity.
Neutral oil: Avocado or light olive oil keeps the dough soft without overpowering the flavor.
Fine sea salt: Enhances the nuttiness of the wheat without making the tortillas taste “salty.”

A full ingredient list and quantities can be found in the recipe card below.

Tools You May Need

Grain mill

Cast iron pan or griddle

Rolling pin – I find a handheld rolling pin the easiest way to roll out tortillas.

How To Make The Best Whole Grain Tortillas

Mix dry ingredients: In a large bowl, whisk together the freshly milled flour, salt, and baking powder.
Add liquid ingredients: Combine warm water, oil, and vinegar, and pour into the dry ingredients. Mix until all the flour has been incorporated.
Rest: Allow the dough to rest for 10-15 minutes. It will be sticky, but the flour will start to absorb the liquid as it sits.
Knead: Turn the dough out onto a clean surface and knead by hand for about 5 minutes, until smooth.
Rest the dough: Cover the dough with a damp towel or wrap in beeswax wrap and let it rest at room temperature for 15 minutes. This helps the bran hydrate and gluten relax, making it easier to roll out.
Divide and roll: Divide dough into 12 equal pieces (about 55g each). Roll each into a ball, then place it back in an oiled bowl while you roll the others. This mini rest helps get a pliable tortilla! flatten into a disc. Roll each dough ball into a thin circle about 18–20 cm wide. If you find it sticks when you try and pick it up, roll on a lightly oiled surface.
Cook: Heat a dry cast iron skillet or griddle over medium-high to medium heat. Once hot, cook each tortilla for about 30–45 seconds per side, or until you see bubbles and golden spots. Stack cooked tortillas in a clean kitchen towel to keep warm and soft (this is important for pliable tortillas!).

Fresh tortillas on a white plate with flour and wheat beside.

Recipe Tips

Rest the dough: This allows the bran to hydrate and makes the tortillas easier to roll. You can rest the dough for up to an hour.
Keep your skillet hot: Medium-high heat is ideal for those signature brown spots.
Store properly: Wrap cooled tortillas in a towel or airtight container to keep them soft. To freeze, tack cooled tortillas with parchment in between and freeze in a zip-top bag. Reheat on a skillet or in the oven.

Best Whole Grain Tortillas Variations

Sourdough whole grain tortillas: Use discard or a bit of starter for added depth. Or try my sourdough tortilla recipe with all-purpose flour for a different fresh homemade tortilla option.
Store-bought whole wheat flour: Works too! Use the same weight but sift if it’s too coarse so you get soft tortillas in the end.
Spelt tortillas: Sub freshly milled spelt flour for a slightly sweet, softer tortilla.
Herbed tortillas: Add dried herbs like oregano or rosemary to the dough for extra flavor. These are a favorite for sandwich wraps, loaded with plenty of vegetables and some protein.
Tortilla pizza crusts: If you have a lot of tortilla left over, make a crispy pizza with them. Place tortillas on a baking sheet, top with sauce, cheese and your favorite toppings. Bake a few minutes—just until cheese is melted.

Best Whole Grain Tortillas FAQs

The healthiest tortillas are made at home using freshly milled flour. Whole wheat tortillas are considered better (even than white corn tortillas) because they contain more fiber and nutrients.

Whole grains are generally considered to be better since they have more nutrients. Whole wheat flour from the store has lost most of its nutritional value once we purchase it.

They may be overcooked or the dough was too dry. Try a shorter cook time or let the dough rest longer.

While all freshly milled grains are better for you (especially compared to white bread!), amaranth has more grams of protein (g protein) and buckwheat is high in fiber (g fiber). Ancient grains like Einkorn or Khorasan are honorable mentions and usually work well for gluten-sensitive people.

I hope you love this recipe!