Fresh Milled Flour Apple Cinnamon Streusel Muffins
These Fresh Milled Flour Apple Cinnamon Streusel Muffins are one of my favorite muffins. They’re soft, filled with little chunks of fresh apples, and topped with a yummy cinnamon streusel!
Are you looking for more Freshly Milled Flour Recipes? Try our Pumpkin Muffins, Einkorn Chocolate Banana Muffins, or Cinnamon Sugar Donut Muffins, all made with whole grains!

We love apple cinnamon recipes. My Apple Cinnamon Cream of Wheat and Fried Apples are two of our favorites, and these muffins definitely don’t disappoint!
One of my favorite things about baking with freshly milled flour is that you don’t have to give up the muffins and treats you love! You get all the benefits of whole grains, and these muffins are every bit as soft and tender as you’d expect. Not to mention soooo delicious!
What you’ll love about these Apple Cinnamon Muffins
Recipe Ingredients:
You’ll need the following ingredients to make this whole wheat apple muffin recipe:
- Freshly Milled soft white wheat flour
- Freshly Milled hard white wheat flour
- Light brown sugar
- White sugar
- Baking powder
- Baking soda
- Cinnamon
- Salt
- Eggs
- Buttermilk
- Butter
- Vanilla extract
- Granny Smith apples

Ingredient Notes:
- Fresh Milled Flour: I use mostly soft white wheat for a tender muffin, with a little hard white wheat for extra structure.
- Apples: I prefer using Granny Smith because they’re tart and hold their shape well during baking.
- Buttermilk: Use real, full-fat buttermilk for the best results. I don’t recommend the homemade milk and vinegar substitute because it’s much thinner than real buttermilk and can change the texture of your muffins.
How to make Fresh Milled Flour Apple Cinnamon Streusel Muffins
Grab the full recipe card with exact ingredient amounts below
Step 1: Preheat the oven to 375°F. Line a 12-cup muffin pan with paper liners or grease the cups.
Step 2: In a small bowl, combine the brown sugar, freshly milled soft white wheat flour, and cinnamon for the streusel. Cut in the cold butter until coarse crumbs form. Refrigerate while preparing the muffin batter.
Step 3: In a large bowl, whisk together both freshly milled flours, brown sugar, granulated sugar, baking powder, baking soda, cinnamon, and salt.
Step 4: In a separate bowl, whisk together the eggs, buttermilk, melted butter, and vanilla extract.
Step 5: Pour the wet ingredients into the dry ingredients and gently stir until just combined. Fold in the diced apples.
SAVE THIS RECIPE FOR LATER!
Step 6: Divide the batter evenly among the 12 muffin cups. Sprinkle the chilled cinnamon streusel over the tops without pressing it into the batter.
Step 7: Bake at 375°F for 17–20 minutes, until the toothpick inserted into the center comes out with a few moist crumbs.
Step 8: Cool in the muffin pan for 5 minutes before transferring to a wire rack. If using the vanilla glaze, whisk together the powdered sugar and milk until smooth and drizzle over the cooled muffins.
NOTE: The flour measurement is for the flour after the wheat berries have been milled. I never use flour while it is still warm from the mill. Place it in the freezer to cool before adding it to the dough.

PRO TIP:
Don’t over mix the batter! Stir just until the dry flour disappers, then gently fold in the apples. Over mixing can make muffins tough. Let the muffins cool before removing the paper liners so they have time to firm up.

Storage and Reheating:
Storage: Store cooled muffins in an airtight container at room temp for up to 2 days.
Reheating: Microwave for 10-15 seconds if you prefer a slightly warm muffin.
Freezing: Allow the muffins to cool completely, then freeze in a freezer safe container or bag for up to 3 months. Thaw at room temperature before serving.

Additions and Substitutions:
- Apples: Honeycrisp or Pink Lady apples can be used instead of Granny Smith for a sweeter muffin. I would decrease the sugar some.
- Nuts: Add 1/2 cup chopped pecans or walnuts for a little crunch.
- Glaze: Add the glaze or leave it off! The cinnamon streusel adds plenty of sweentness!
- No streusel: Sprinkle a little cinnamon sugar over the tops before baking instead.
FAQs about this Apple Cinnamon Streusel Muffins with Fresh Milled Flour
Can I use all Soft White Wheat Flour?
Yes! You can use all soft white flour. I tested it out and they were fine, just a little more delicate. They crumbled more with all soft white. I prefer adding a small amount of hard white for structure.
Do I need to peel the apples?
I recommend peeling them for the softest texture. Granny Smith apple skins can remain a little firm after baking.
Why are my apple muffins falling apart?
Muffins are more delicate when they’re fresh from the oven, especially with pieces of apple throughout. Let them cool before removing the liners so they have time to set. (In all transparency, we never wait that long, LOL!)
What can I serve with these whole grain Apple Cinnamon Muffins?
These muffins are so good with a cup of coffee, tea, or a tall glass of milk! For a bigger breakfast, serve them with scrambled eggs, bacon, sausage, or fruit.
Ready to Bake More with Fresh Milled Flour
If you’re ready to do more with freshly milled flour, check out my Complete Guide To Freshly Milled Flour. It has everything I wish I had when I first started milling my own flour!
You can also grab my Handheld Bites eBook, where One Fresh Milled Master Dough can be turned into 10 different handheld meals that are perfect for lunches, quick dinners, and meal prep!
Made this recipe? I’d love to see it! Tag me on IG or FB @littlechefwithin or share a photo in my Facebook group Fresh Milled Flour Happiness. I love seeing what you’re baking!

Fresh Milled Flour Apple Cinnamon Streusel Muffins
Equipment
Ingredients
Muffins
- 220 g freshly milled soft white wheat flour
- 30 g freshly milled hard white wheat flour
- 60 g light brown sugar packed
- 110 g granulated sugar
- 7 g baking powder
- 3 g baking soda
- 3 g ground cinnamon
- 3 g salt
- 2 large eggs room temperature
- 110 g full-fat buttermilk
- 6 Tbsp salted butter melted and slightly cooled
- 5 g vanilla extract
- 190 g Granny Smith apples peeled and diced into 1/2″ pieces
Cinnamon Streusel Topping
- 50 g light brown sugar
- 35 g freshly milled soft white wheat flour
- 2 g ground cinnamon
- 2 Tbsp cold salted butter
Vanilla Glaze (Optional)
- 60 g powdered sugar
- 2-3 tsp milk 2–3 tsp
Instructions
- Preheat the oven to 375°F. Line a 12-cup muffin pan with paper liners or grease the cups.
- Prepare the streusel by combining the brown sugar, flour, and cinnamon in a small bowl. Cut in the cold butter with a fork or pastry cutter until coarse crumbs form. Refrigerate while preparing the muffin batter.50 g light brown sugar,35 g freshly milled soft white wheat flour,2 g ground cinnamon,2 Tbsp cold salted butter.
- In a large bowl, whisk together both freshly milled flours, brown sugar, granulated sugar, baking powder, baking soda, cinnamon, and salt.220 g freshly milled soft white wheat flour,30 g freshly milled hard white wheat flour,60 g light brown sugar,110 g granulated sugar,7 g baking powder,3 g baking soda,3 g ground cinnamon,3 g salt.
- In a separate bowl, whisk together the eggs, buttermilk, melted butter, and vanilla extract.2 large eggs,110 g full-fat buttermilk,6 Tbsp salted butter,5 g vanilla extract.
- Pour the wet ingredients into the dry ingredients and gently stir until just combined. Fold in the diced apples. Do not over mix.190 g Granny Smith apples.
- Divide the batter evenly among the 12 muffin cups, filling each about 3/4 full. Sprinkle the chilled streusel evenly over the tops without pressing it into the batter.
- Bake for 17–20 minutes, or until the tops spring back lightly when touched and a toothpick inserted into the center comes out clean or with a few moist crumbs.
- Let the muffins cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.
Optional Vanilla Glaze
- Whisk together the powdered sugar and milk until smooth, adding just enough milk to make a thick but pourable glaze.60 g powdered sugar,2-3 tsp milk.
- Drizzle lightly over the cooled muffins.
Nutrition
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About Vicky Hadley
Vicky Hadley is a professional food photographer and creator behind Little Chef Within. As a mom of 6 boys, there’s always plenty of noise and plenty of food! She relies on filling meals to keep her crew happy and loves creating recipes that real families can count on.


