Cinnamon Apple Muffins Recipe with Fresh Milled Flour

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Cinnamon apple muffins made with fresh milled flour. Friends and family request these constantly. If you only make one muffin this season, make it this one!

A stack of several apple cinnamon muffins made with fresh milled flourA stack of several apple cinnamon muffins made with fresh milled flour

Fall is right around the corner and these cinnamon apple muffins could not be a more perfect Autumn treat. From the first bite, you’ll know this recipe is a keeper.

You can believe me when I say that this is a most-loved and most-requested recipe here at the Lavender Blue Cottage. It checks all of the boxes – incredible flavor, great texture and fabulous nutrition. In other words, apple cinnamon muffin perfection!

Special Announcement: My 100% Whole Wheat 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 my Keeper of the Home Cookbooks.

A serving plate filled with apple cinnamon muffins, some featuring a streusel toppingA serving plate filled with apple cinnamon muffins, some featuring a streusel topping

Fresh Milled Flour Makes the Best Muffins

If you know me, you’ll know I love freshly milled flours. I mill all of my flour from wheat berries. It’s a quick and easy process that you can read about in how to mill your own flour and the health benefits.

Fresh milled flour is the best kept secret in baking. In a nutshell, you get the best flavor and the most nutrients from your flours within the first hours and days after they are milled. Quality declines significantly after that.

You have no way of knowing how long a bag of flour has been sitting on your grocery store shelf. That’s why I use fresh milled flour for muffins and everything else. It’s top quality every time!

For tips on how to get perfect muffins every time, checkout my muffin making tips.

Now, let’s get started!

Cinnamon Apple Muffins Ingredients

Wet Ingredients

  • ½ cup plain yogurt
  • ½ cup applesauce (sugar free)
  • 2 tablespoons apple juice or apple cider
  • 2 eggs
  • ⅓ cup honey
  • 2 tablespoons pure maple syrup
  • ⅓ cup melted and cooled coconut oil or butter (or ¼ cup butter + ¼ cup coconut oil)
  • 1 teaspoon pure vanilla extract

Dry Ingredients

  • 2 ¼ cups (290 grams) freshly milled flour 
  • 1 teaspoon salt
  • 2 teaspoons cinnamon
  • ¼ teaspoon nutmeg
  • ¼ teaspoon cloves
  • ¼ teaspoon allspice 
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
A bowl holds muffin batter and finely diced pieces of appleA bowl holds muffin batter and finely diced pieces of apple

Mix-Ins

  • 1 cup peeled and finely diced apple (about 1 large apple)
  • 1 tablespoons flour (to coat the apples)

Optional Streusel Topping

  • ¼ cup (30 grams) freshly milled flour
  • ¼ sugar
  • 1 teaspoon cinnamon
  • Pinch of salt
  • 2-3 tablespoons cold butter

How to Make these Cinnamon Apple Muffins

Preheat your oven to 425°F (220°C). Grease a muffin tin or line it with muffin liners and set aside.

In a large bowl, whisk together all of the wet ingredients until smooth and well combined.

Add the freshly milled flour, salt, cinnamon, nutmeg, cloves and allspice to the bowl with the wet ingredients. Gently stir just until incorporated. Cover and set aside to let the flour absorb the liquid for 10 minutes.

While resting the batter, make the streusel topping (if desired) by combining the flour, sugar, cinnamon, salt and cold butter in a small bowl.  Use a fork or your fingers to bring it together into a dry, crumbly mixture.  Set aside.

After resting, sprinkle the baking powder and baking soda into the muffin batter. Mix gently until everything is evenly combined, being careful to avoid overmixing.  

Toss the diced apple slices in the tablespoon of flour, until coated.  This will help the fruit not sink to the bottom.  Fold the apples into the batter.

Working quickly, spoon the muffin batter into the prepared muffin pan, filling each cup evenly.

If adding the streusel topping, sprinkle over each muffin, gently pressing the crumb toppings into the batter.

A muffin tin holds muffins made with apple, cinnamon and freshly milled flourA muffin tin holds muffins made with apple, cinnamon and freshly milled flour

Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 7-9 minutes, or until the centers feel firm and the muffins are baked through.

Remove from the oven and let cool slightly on a wire rack.

Printable Cinnamon Apple Muffin Recipe Card

Cinnamon Apple Muffins with Fresh Milled Flour

Created by The Keeper of the Home

Delicious and moist apple cinnamon muffins made with fresh milled flour. Need I say more? This is a family favorite recipe!

Wet Ingredients

  • ½ cup plain yogurt
  • ½ cup applesauce (sugar free)
  • 2 tablespoons apple juice or apple cider
  • 2 eggs
  • ⅓ cup honey
  • 2 tablespoons pure maple syrup
  • ⅓ cup melted and cooled coconut oil or butter (or ¼ cup butter + ¼ cup coconut oil)
  • 1 teaspoon pure vanilla extract

Dry Ingredients

  • 2 ¼ cups (290 grams) freshly milled flour
  • 1 teaspoon salt
  • 2 teaspoons cinnamon
  • ¼ teaspoon nutmeg
  • ¼ teaspoon cloves
  • ¼ teaspoon allspice
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda

Mix-Ins

  • 1 cup peeled and finely diced apple (about 1 large apple)
  • 1 tablespoons flour (to coat the apples)

Optional Streusel Topping

  • ¼ cup (30 grams) freshly milled flour
  • ¼ sugar
  • 1 teaspoon cinnamon
  • Pinch of salt
  • 2-3 tablespoons cold butter
  • Preheat your oven to 425°F (220°C). Grease a muffin tin and set aside.

  • In a large mixing bowl, whisk together all of the wet ingredients until smooth and well combined.

  • Add the freshly milled flour, salt, cinnamon, nutmeg, cloves and allspice to the bowl with the wet ingredients. Gently stir just until incorporated. Cover and set aside to let the flour absorb the liquid for 10 minutes.

  • While resting the batter, make the streusel topping (if desired) by combining the flour, sugar, cinnamon, salt and cold butter. Use a fork or your fingers to bring it together into a dry, crumbly mixture. Set aside.

  • After resting, sprinkle the baking powder and baking soda into the batter. Mix gently until everything is evenly combined, being careful not to overmix.

  • Toss the diced apple slices in the tablespoon of flour, until coated. This will help the fruit not sink to the bottom. Fold the apples into the batter.

  • Working quickly, spoon the batter into the prepared muffin tin, filling each cup evenly.

  • If adding the streusel topping, sprinkle over each muffin, gently pressing the crumbs into the batter.

  • Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 7-9 minutes, or until the centers feel firm and the muffins are baked through.

  • Remove from the oven and let cool slightly on a wire rack.

Did you make this?

Make sure to follow The Keeper of the Home on Instagram and Pinterest for more creative ideas!

Storing Cinnamon Apple Muffins

Store cooled muffins in an airtight container at room temperature for up to 2 days. For longer storage, wrap each muffin with plastic wrap and place in a freezer safe container or bag. Freeze the muffins the same day they’re baked. Thaw at room temperature before serving.

Where to Get Baking Supplies

If you need baking supplies, checkout the 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!

A plate hold apple cinnamon muffins next to a couple of ripe applesA plate hold apple cinnamon muffins next to a couple of ripe apples

More About Muffins

Cinnamon apple muffins are perfect for Fall or any time of year. Moist, healthy and delicious, these muffins will be requested over and over again. Make yourself a batch today!

For more muffin tips and great recipes, try:

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