Last Updated on May 19, 2026 by Michelle

Muffins were one of the first “successful” things I made with fresh milled flour.

With blueberry muffins always being a hit around here, I was determined to make fresh milled flour blueberry muffins right off the bat. Granted, I didn’t open up my grain mill and make good muffins right away, but after a few attempts, once Bill said “keep this recipe!,” I knew I had created a keeper.

Why use fresh milled flour?

Instead of feeding your family “regular” homemade muffins for breakfast or as a snack, why not offer them superfood blueberry muffins, just by changing what flour you’re using? Using fresh milled flour turns normal muffins into a multi-vitamin, offering your body so many nutrients.

Regular all-purpose flour from the store? It’s so old and processed that it’s essentially just nutrient-less starch to your body. Fresh milled flour? A complex, nutrient-packed flour that folks swear doesn’t spike their blood sugar. Even though fresh milled flour blueberry muffins are still, well, muffins, they’re something you can feel amazing about feeding your family.

Learn about my top 5 benefits to milling fresh flour.

Can you make muffins with fresh flour?

Absolutely.

I’d argue that fresh flour makes the best muffins!

While this recipe is super straightforward, there are a few things to keep in mind. Fresh milled flour behaves differently than store bought flour does, given the fact that it’s a whole grain flour. It’s packed full of antioxidants, protein, and minerals, but the bran and germ that make it nutritious can also make muffins dense, gummy, or not rise.

This recipe uses soft white wheat to keep it simple and straight forward (if you own a grain mill, you most likely have soft white wheat berries in your pantry), but if I’m feeling fancy I’ll swap the soft white wheat for einkorn, Khorasan (kamut), or barley (or a mixture).

How to make fresh milled, gluten-free blueberry muffins

If you’re looking to make gluten-free muffins with fresh milled flour, try using oat groats, milled into fine flour (don’t mill rolled oats!). For better texture, add 2-3 teaspoons of a starch to the muffin batter. Some starches could include:

Arrowroot powder

Cornstarch (or a chickpea alternative)

Tapioca starch

Fluffy fresh milled muffins: tips & tricks

I’ve picked up some tips for making better muffins throughout the years. Some are fresh flour specific, and some can be applied to any recipe, made with any flour.

Fill your muffin tins/liners enough. You want them to be about 2/3-3/4 full to achieve tall, bakery-style muffins.
Don’t skip the dairy. Using sour cream, Greek yogurt, or thick buttermilk will help your muffins stay soft, non-crumbly, and retain their moisture/softness for longer.
Don’t lessen the sugar too much. Turns out, sugar not only makes muffins taste amazing, but also helps them retain moisture, be tender but not crumbly, rise higher, and brown nicely without burning. If you reduce the sugar too much, you’ll have dry, crumbly muffins that go stale very quickly.

If you’re struggling with your muffins being gummy in the center, try letting your batter sit for 10-15 minutes before baking. You’ll find that this recipe doesn’t specifically call for letting the batter sit–because I simply don’t find it necessary and I’m usually eager for a fresh-from-the-oven muffin ASAP. But try adding this step if your muffins don’t come out as well as you’d like.
Don’t overmix your batter. Just make sure there aren’t any huge lumps or pockets of flour at the bottom of your bowl, and you’re good to go. Mixing your batter too much will make muffins tough, as you’re actually developing gluten, which we want in bread dough but want to avoid in muffin batter.
Don’t overbake your muffins. As soon as the centers are set, remove them from the oven and let them cool. If you want to use an instant read thermometer, cooked muffins temp at 190-200 in the center.

The best blueberry muffins are made with fresh milled flour

If you’re looking to upgrade your classic blueberry muffins, look no farther than making them with fresh milled flour.

Not only does whole grain flour simply taste better, it also offers a depth of flavor that isn’t easy to explain. If you’ve ever used whole wheat flour from the store, ditch that thought in your mind. Plastic-y, stale, playdough-y is what comes to my mind. Fresh milled flour is a whole different story. Rich, nutty, buttery, wheat-y tasting–yes–but in the best, warm way.

The soft sweetness of muffins pairs so well with the rich flavor of fresh milled flour. Trust me, once you try them you can’t go back. Especially cut in half, grilled in a hot cast iron skillet with butter? Forget about it.

How to prevent dense whole wheat muffins

When we think of words like “whole wheat,” “whole grain,” or “stone-ground,” we often think “dense, heavy, crumbly.” But that doesn’t have to be the case. With this recipe, and a few thoughts to help you adapt any muffin recipe you should ever want to make, you’re well on your way to whole wheat muffins that break all the serotypes.

Use the right ingredients. Adding ingredients like Greek yogurt/sour cream, buttermilk, liquid oil, eggs, all combine into a magical creation: soft, moist whole wheat muffins that makes everyone ask for the recipe.
Use the right flour. Make sure to stick with soft grains, or ancient grains (with lower gluten potential) for the best muffins. Using hard grains (like hard white wheat) will result in more gluten forming in the muffin batter, leading to tough muffins. No thanks.
Bake at the right temperature. If your oven runs cold, consider upping the temperature by a few degrees. You really want a nice, pre-heated oven, hot and ready to go when your muffins go in. If the oven is still preheating, or the temperature is running low, your muffins won’t rise quite as high.
Add toppings. The texture of coarse sugar or a nice streusel not only adds a bakery-style touch, but also helps improve the texture of the muffin overall.

What wheat berries make the best muffins?

Almost any wheat berry can be used to make muffins. However, softer grains (soft white wheat), and ancient grains (einkorn, spelt, khorasan) will make better muffins than harder grains (hard white, hard red, durum).

Best wheat berries to make muffins:

Soft white wheat

Einkorn

Khorasan/Kamut

Spelt

Wheat berries to NOT use in muffins:

(These grains can be used, but for best results, mix 50/50 or even 25/75 with a grain listed above.)

Hard white/hard red

Durum

Rye

Print Recipe

The best fresh milled flour blueberry muffins

Servings: 12 muffins

Ingredients

2 ¼ cups soft white flour
¾ cups coconut sugar*
2 teaspoons baking powder
½ teaspoon salt
2 eggs
¾ cup greek yogurt or sour cream
½ cup liquid oil
½ cup milk
1 teaspoon either vanilla or lemon extract
1 ¾ cups blueberries either fresh or frozen
Coarse sugar for sprinkling, optional

Instructions

Preheat your oven to 350.
In a large bowl, mix all the muffin ingredients together, except the blueberries. After the batter is mixed well, gently fold the blueberries in.
Ladle batter into greased muffin tins, filling each well about ¾ full.
Sprinkle the tops with sugar, if desired.
Bake for 15-20 minutes, until they’re golden, a toothpick inserted in the middle comes out clean, or a thermometer reads roughly 200 degrees.