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 these days I always grab an ancient or heritage grain, for even more antioxidants in my flour. Feel free to swap the soft white wheat for einkorn, Khorasan (kamut), spelt, 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. 

1. 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.
2. 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.
3. 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.
4. 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

Barley

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

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.

Notes

*If you don't have coconut sugar on hand, substitute traditional cane sugar.

What you’ll need to make blueberry muffins:

More like the best fresh milled flour blueberry muffins:

• How to make rolled oats with an oat flaker (and why you should!)
• Whole wheat pumpkin muffins
• The best sandwich bread with fresh milled flour
• Wheat berries: everything you need to know

Shop all my favorite grains and wheat berries here, and shop grain mills here.

Follow along on my fresh milled flour adventures on Instagram (@souly.rested) and Facebook.

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Whole wheat pumpkin muffins

The brown sugar filing hovers perfectly in the center of these soft, just-sweet-enough pumpkin muffins. Then they’re all topped off with a crunchy-yet-soft streusel topping. Then the icing on the cake (literally!!) is the sweet maple glaze drizzled over the top.

If you don’t mill your own flour yet, no worries! (Although, I gotta ask… what’s stopping you?) This recipe will work well with regular ol’ all-purpose flour as well.

Can whole wheat pumpkin muffins be healthy?

Even though these are definitely a treat, with the addition of whole wheat flour, these pumpkin streusel muffins are packed full of vitamins, minerals, and they’re also higher in protein and fiber than if they were made with white flour.

Fresh milled flour actually contains all three parts of the wheat berry, including the bran and germ, which are powerhouse foods! Learn more about fresh milled flour here: Why I started milling my own flour.

Bonus: these muffins are made with coconut sugar, a complex, all-natural sugar, which will leave you feeling more full and without the energy crash of junky refined sugars. Learn more about sugars here: The best sugars to use.

Are muffins healthy or unhealthy?

Because these muffins are made with all-natural sugars, freshly milled flour, and zero preservatives, they’re actually a healthy snack.

But I can’t say the same thing about the muffins you order at your favorite coffee shop, or the ones you pick up in the grocery story bakery. Those have to stay moist and fresh for days (heck, sometimes weeks), so they’re loaded with all these preservatives I can’t pronounce, from mono and diglycerides, to sodium stearoyl lactylate, sorbitan monostearate, polysorbate 60, gelatinized wheat starch, and carnauba wax.

I don’t think you have to have a degree in food science to know which option is going to be a much better choice.

Bonus: these homemade muffins genuinely taste better.

How to make whole wheat pumpkin muffins with a brown sugar filling

Cocoa powder is my secret weapon for making your muffin filling more visible (and we all know your tastebuds start with your eyes!). You don’t taste the chocolate flavor since there’s not much cocoa powder in the filling, but it’s just enough to allow the bright color of the filling to shine throughout the muffin. Swirling the filling through the batter just allows the filling to stay put and not remain a dry lump of sugar, but instead transform into a gooey, lovely filling while the muffins bake.

Whole wheat pumpkin muffins recipe

INGREDIENTS

Streusel topping:

• 1/3 cup coconut sugar
• 3/4 cup flour*
• 1 teaspoon ground cinnamon
• 4 tablespoons melted butter, lard, or coconut oil

Brown sugar filling:

• 1/3 cup coconut sugar
• 1.5 teaspoons ground cinnamon
• 1 teaspoon cacao powder (for color)
• 1 teaspoon sorghum syrup (or molasses)

Pumpkin muffin batter:

• 1/3 cup avocado oil, or other neutral-flavored oil
• 1 cup pumpkin puree
• 1 cup coconut sugar
• 2 eggs
• 1 teaspoon ground cinnamon
• 1/4 teaspoon ground ginger powder
• 1/4 teaspoon ground nutmeg
• generous pinch salt
• 2 teaspoons baking powder
• 1 1/2 cups flour*

Maple glaze:

• 2 tablespoons maple syrup
• powdered sugar, to desired consistency

DIRECTIONS

1. First, mix the streusel topping. Combine the dry ingredients, then pour in the melted butter and stir until a moist crumble forms. Set in the fridge to cool.
2. Next mix the brown sugar filling. Combine everything in a small bowl, incorporating the molasses as best you can–some chunks are ok. Set aside.
3. For the pumpkin muffin batter, combine everything but the flour into a large mixing bowl, and mix until combined. Add the flour and stir until just combined.
4. Assemble the muffins by filling each hole of a muffin tray 1/2 full of batter (I find half a muffin is about 1 tablespoon). This recipe should make exactly 12 muffins, so fill 12 holes 1/2 way. Then sprinkle the brown sugar filling mixture evenly over all 12 muffins. Cover that with the remaining muffin batter so each muffin is filled. Carefully swirl a toothpick through each muffin to settle the filling into the batter, but don’t overmix.
5. Generously sprinkle the streusel topping over all the muffins.
6. Bake at 350 for 25 minutes, or until the internal temperature in the middle of the muffins reads about 200 degrees.
7. Set them aside to cool slightly, and mix the maple syrup and powdered sugar until it’s thick but drizzle-able.
8. When the muffins are mostly cool, drizzle the maple glaze all over the tops and enjoy!

*I like to use fresh milled Spelt flour for the streusel topping and Soft White Wheat flour for the pumpkin muffin batter.

The four grain mills I use and recommend

If you’re considering investing in a grain mill, find out the questions you need to ask in the Ultimate Guide to Choosing a Grain Mill.

More like whole wheat pumpkin muffins:

• Wheat berries: everything you need to know
• Kamut chocolate chip cookies
• Fluffy 100% whole wheat dinner rolls
• Lasagna noodles with fresh milled flour
• Why I started milling my own flour

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