This post may contain affiliate links, which means I get a small percentage of the sale at no extra cost to you. I only recommend items I love and have had a positive experience with. Thank you!
No gatekeeping here! I’m sharing my muffin making tips for a tall rise, perfect shape and incredible texture when baking with fresh milled flour.

If you’ve found yourself loving the world of freshly milled flour recipes, you are my kind of people.
If you’ve found yourself frustrated that those delicious and healthy fresh milled flour recipes don’t behave exactly the same way as their white flour counterparts, you are also my people.
I’ve spent lots of time trying to get the qualities I love from white flour muffin recipes to translate to whole grain fresh milled flour recipes. To be specific, I’ve been after a gorgeous muffin shape with a nice tall rise. That’s tricky to do when working with fresh milled flour, but not impossible.

Let me show you my tricks for getting tall bakery-style muffins with moist crumbs. You don’t need to sacrifice nutrition. You just need the right technique.

Table of Contents

I Wrote a Cookbook!
Special Announcement: My 100% Whole Grain Yeast Breads with Freshly Milled Flour cookbook is now available! It contains my best-of-the-best yeast bread recipes and lots of great information about milling flour and baking with whole grains. Get your copy today or check out all of my Keeper of the Home Cookbooks.
Understanding Freshly Milled Flour
When it comes to flour, fresh is best. Milling flour from wheat berries is 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 best flavor and the most vitamins, minerals and nutrients from your flours within the first hours and days after they are milled. That fresh milled flour will produce fabulous muffins, but it can behave differently from store-bought flours. You may notice more density, less rise and a flat top.
Here is how we fix that.

Muffin Making Tips with Fresh Milled Flour
Use the Right Leaveners
- Fresh milled flour muffins need both baking soda and powder in the dry ingredients. Baking soda reacts with acidic ingredients to produce rise. Baking powder will react with the oven heat to do the same.
- Don’t go overboard with the leavening agents or you’ll get a metallic taste. My favorite plain muffin recipe uses 3/4 teaspoon baking soda and 1 teaspoon baking powder, which is perfect.
Hydration is Key
- Fresh flour contains less moisture than store-bought flour, so it needs more time to absorb liquid.
- After combining wet and dry ingredients, let the muffin batter rest in the bowl for about 10 minutes. This makes a big difference.
Mix Lightly
- The coarser texture of fresh milled flour can cause less rise.
- Fresh flour will develop gluten structure more quickly than white flour.
- Only do light mixing of your muffin batter, stirring as little as possible.

Adjust Fill Level
- Fill your muffin pan with enough batter to compensate for less rise.
- Aim for cups that are 3/4 to nearly full is a good estimate.
Change Your Oven Temperature
- Start baking your muffins at high temperature, then turn your oven to a lower temperature.
- Bake at around 425 degrees Fahrenheit for the first 5 minutes, then drop to 350 degrees Fahrenheit.
- Remember to lower the oven temperature partway through cooking. If you forget to turn it down, the muffins will cook and brown faster, and possibly be undercooked in the center of the muffin.
- This blast of high heat in the beginning helps the baking powder do its job.
The Ultimate Muffin Recipe
I know you’re probably thinking that now you need a fresh flour muffin recipe to try all these tips on. I highly recommend my basic muffin recipe with fresh milled flour. It’s delicious in its basic form, but it’s also the perfect recipe to personalize. You can try it with your favorite add-ins, toppings, and spreads for some crazy good homemade muffins.

Muffin Making Supplies
If you need baking supplies, checkout my Bread 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!
Learn More About Baking with Fresh Milled Flour
Follow these muffin making tips for a perfect muffin with fresh milled flour. Your tall bakery-style muffins will taste like dessert, but be healthy enough for breakfast.
Just remember to make some extra. Fresh flour muffins disappear quickly!
To learn even more about baking with fresh milled flour try one of these:
- Best Grains for Fresh Milled Flour Muffins
- Should You Use Milk, Buttermilk, or Yogurt in Muffins?
- Melt in Your Mouth Fresh Milled Flour Biscuits
- The Best 19 Fresh Milled Flour Bread Recipes
- Fresh Milled Whole Wheat Flour Waffles Recipe
- Greatest Pancake Recipe with Fresh Milled Flour
- Delicious Fresh Milled Flour Tortillas

Discover more TIDBITS
Love this article? Make sure to connect with me on your favorite social platform below, and leave a comment so we can chat!