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You can make fresh milled flour muffins with many different grains. These are my favorite grains to use and I’ll tell you why.

Growing up, I always adored bakery muffins. They have incredible flavor and a divine texture that muffins from a mix just can’t duplicate. Even homemade muffin recipes don’t compare. A typical homemade muffin recipe usually call for all purpose flour, which is great for many things, but not ideal for light and tender baked goods.
Getting specific with what grain flour you use is one trick I’ve learned for better tasting and perfectly textured muffins. There are lots of options out there. Each one has unique properties that can give your baked goods just what you’re looking for. It’s the difference between a “regular” muffin and a “this is absolutely incredible!” muffin.
I’m going to share my top favorite grains to use for baking muffins. As always, I’m talking about using a freshly milled whole grain flour version of these grains. I’ll explain why that matters below.
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Fresh Milled Flour is Best for Muffins
If you know me, you’ll know I love freshly milled flours. I mill all of my flours at home from whole grains. It’s a quick and easy process that you can read about in how to mill your own flour and the health benefits.
In a nutshell, you get the absolute best flavor and the highest nutritional content from your flours within the first hours and days after they are milled. Quality declines quickly after that.
Milling your own flour opens up a world of possibilities for using different grain types and making custom flour blends. It’s my favorite baking secret for muffins and everything else!
The Best Grains to Mill For Muffins
Speaking of muffins, these are the grains I like to mill for flour whenever I bake muffins:
#1) Soft White Wheat
Soft white wheat tops my list of favorite grain to use for fresh milled flour muffins. It’s a bakery standard for good reason!

Why Soft White Wheat Works
- Naturally mild and slightly sweet flavor
- Lower protein content for a tender crumb
- Produces light-colored baked goods
- Texture of bakery-style muffins
Tips for Soft White Wheat Muffins
- Use fresh milled flour (of course)
- Be prepared to add slightly more liquid to your traditional recipe, as fresh milled flours tend to absorb more liquid than store-bought flours
- Use dairy products like plain yogurt, melted butter or buttermilk to add tenderness and to activate the baking soda
- Let the batter rest 10-15 minutes after mixing to absorb liquid and become airy
- Don’t overmix, a few lumps in the muffin batter are ideal
#2) Einkorn
Einkorn is next of my list of favorite grains to use in muffins. It’s an ancient grain that is super nutritious and tasty. I love baking with einkorn!

Why Einkorn Works
- Naturally sweet and buttery flavor
- Creates moist baked goods
- Gorgeous golden color
- Easy to digest, even for sensitive stomachs
- Weak gluten structure = soft and tender muffin texture
Tips for Einkorn Muffins
- Be prepared to use less liquid than your traditional muffin recipe
- Mix very gently and avoid overmixing
- Let the muffin batter rest 5-10 minutes before baking in the oven
- Don’t add too many mix-ins, as they can weigh down einkorn muffins (shoot for 1-1.5 cups per 12 muffin batch)
- Do use in recipes with moist ingredients like pumpkin puree, applesauce, mashed bananas, etc.
#3) Spelt
Spelt is another grain that makes fabulous muffins.

Why Spelt Works
- Easy to work with and beginner friendly
- Nutty flavor that is sweet and mild
- Makes soft and tender baked good
- Develops more gluten structure and holds its shape better than einkorn
Tips for Spelt Muffins
- Don’t overmix the batter
- Allow the batter to rest 10-15 minutes before baking
- Use fatty acid ingredients like sour cream, kefir or yogurt for extra moistness
- Don’t over bake, a few crumbs left on a toothpick after poke-testing is perfect
#4) Kamut
Ever tried kamut? It has wonderful flavor that makes great muffins!
FYI: Kamut is also known as Khorasan. They are one and the same.

Why Kamut Works
- Gives baked goods a soft texture
- Great buttery and sweet flavor
- Lots of minerals and nutrients
Tips for Kamut Muffins
- Reduce sugar slightly, kamut is sweet
- Let the batter rest 10-15 minutes before baking
- Add moisture rich ingredients like yogurt, pumpkin puree or mashed banana
- Mix gently and don’t over mix
#5) Emmer
Emmer is a little different from the other grains, but it makes a great, filling muffin. Perfect for a quick breakfast or snack.

Why Emmer Works
- Hearty “old fashioned” texture
- Produces moist muffins
- Lots of flavor, slightly sweet
- Rich, darker color than other flours
Tips for Emmer Muffins
- Let the batter rest after mixing for at least 10-15 minutes to absorb moisture (you can even mix the flour and wet ingredients in a bowl and let sit overnight before adding the rest of the dry ingredients)
- Use caramel-type sweeteners like honey, brown sugar or maple syrup
- Don’t over bake – their darker color can be deceiving
- Expect a rustic and hearty texture
#6) Custom Grain Blends
Ok, this last one is more of a suggestion and I haven’t tried every grain/flour combination under the sun, but it stands to reason that you can get a nice combination of qualities by using different flour blends in your muffins.
Consider making your fresh milled flour muffins with something like:
- 50% soft white wheat flour + 50% einkorn flour
- 75% soft white wheat flour + 25% oat flour
- 50 % soft white wheat flour + 50 % kamut flour
Basically, experiment with your favorite fresh milled flours to find a blend that you love. It can become your muffin baking secret weapon!
Where to Find Freshly Milled Flour Muffin Baking Supplies and Ingredients
If you need baking supplies, checkout my Break Making Supplies page. It’s where I share information and links to all my baking favorites. Only the best products make in onto this page!
Must-Try Fresh Milled Flour Recipes
I see delicious fresh milled flour muffins in your future. They’re going to be whole grain healthy and oh, so good. No bakery needed, just a few tips for perfect muffins.
Give one of these grains a try in your next batch of muffins. Let me know how it goes!
- Layered Trifle Recipe Made with Freshly Milled Flour
- Melt in Your Mouth Fresh Milled Flour Biscuits
- Delicious Fresh Milled Flour Tortillas
- Simple Basic Muffin Recipe with Fresh Milled Flour
- Fresh Milled Whole Wheat Flour Waffles Recipe
- Greatest Pancake Recipe with Fresh Milled Flour
- Healthy Whole Wheat Cinnamon Rolls
- 100% Whole Grain Sourdough Bread Made Simple
- 100% Whole Grain Einkorn Sourdough Bread Simplified
- 100% Whole Grain Spelt Sourdough Bread

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