These tender, sweet and fluffy homemade Apple Muffins are made with Greek Yogurt. The irresistible spices, sweet streusel topping and tender apples make this one delicious yet healthy breakfast or snack. Each one is filled with nutritious whole grains and come in at 217 calories and 5 grams of protein!

a streusel topped apple muffin up close from the side

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Why You’ll Love These Healthy Apple Muffins

This Healthy Greek Yogurt Apple Streusel Muffin Recipe is made with oats, whole grain flour, and fresh apple. Each muffin comes in at 2 grams of fiber and only 217 calories each. Plus, I used Greek yogurt and eggs, which give each muffin 5 grams of protein!

If you were following along on my Instagram stories, you know that it took me a lot of testing to get these Greek yogurt muffins just right. From the first test, they tasted pretty great, like a donut actually, but I just had the darndest time getting them to rise just so, without losing the moist, soft texture. They also were a little too dark.

I tried changing everything from the leavener, oven temp, the amount of liquid, the amount of flour, and even switching the sweetener.

Eight tries later and they are now—dare I say—perfect!

More Healthy Baking Recipes with Apples

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Ingredient Notes For Our Streusel-Topped Apple Muffins

Streusel topping

  • Oats: we prefer old-fashioned oats but quick oats (instant oats) also work
  • All-purpose flour: to bind the streusel topping
  • Sugar: You will need 2 tablespoons granulated natural cane sugar (evaporated cane juice) or you can sub in another granulated sugar like maple sugar, coconut sugar white sugar or brown sugar.
  • Softened unsalted butter, softened
  • Cinnamon

For The Muffins

  • Kitchen Staples: egg, apple juice, white all-purpose flour, baking soda, baking powder, cinnamon, nutmeg and salt
  • Oil: You can use canola oil, avocado oil or any neutral oil. Really any oil will do as long as it doesn’t have a strong taste or use melted coconut oil or butter.
  • Whole Wheat Flour: For this recipe, we used a blend of white flour with whole wheat flour or white whole wheat flour for a boost of nutritious whole grains.
  • Apple: You’ll want 1 large apple, peeled and diced
  • Greek Yogurt: To lighten the batter and replace some of the fat
  • Cane Sugar: This was key to getting the best texture. The key was switching from our pure maple syrup, which makes baked goods brown more easily, to natural cane sugar (also known as evaporated cane juice). This type of sugar is dry like white sugar, not clumpy, and packable like brown sugar. Can sugar is granulated, but it is still a little brown because it hasn’t been fully refined yet, and still retains some of its natural molasses. The crystals are larger than white sugar—almost as big as turbinado—and it adds a delightful crunch to the streusel topping. If you’re wondering, turbinado is a fine substitute by the way.

How To Make Apple Streusel Muffins

Preheat oven to 375ºF. Coat a 12-well muffin tin with cooking spray or line with paper muffin liners.

Rub together oats, ¼ cup all-purpose flour, 2 tablespoons cane sugar, butter and ½ teaspoon cinnamon with clean fingertips in a small bowl until crumbly.

Whisk egg, yogurt, evaporated cane juice, oil and apple juice in a large bowl until smooth. Whisk 1 cup all-purpose flour, whole-wheat flour, baking powder, 1 teaspoon cinnamon, baking soda, nutmeg and salt in a medium bowl. Add the dry mixture to the wet mixture and stir the muffin batter to combine. Add the apple and stir to combine.

Divide the batter among the prepared muffin tin wells. Top with the streusel, dividing evenly. Transfer to the oven and bake until a toothpick inserted in the center comes out clean, 26 to 28 minutes. Let cool in the pan 10 minutes before removing the muffins from the muffin tin, and transferring to a wire rack to cool.

side view of apple muffins with apples in the background

How To Store, Freeze and Reheat Apple Muffins

  • Keep at room temperature in an airtight container for up to two days.
  • Place in a freezer Ziplock bag and press the extra air out of the bag. Seal shut and freeze up to 1 month.
  • Thaw at room temperature for 10 hours or up to 1 day.
  • For the best texture, we recommend reheating leftover muffins.
  • The fresh apples can make the muffins a little soggy after freezing and thawing. (Especially frozen and thawed muffins.) Warm for 20 seconds in the microwave or in the oven (wrapped in foil) for 10 to 15 minutes at 350 degrees.

Serving Ideas For Apple Muffins

Serve these healthy apple cinnamon muffins with freshly squeezed blood orange juice for a brunch buffet with classic brunch staples like veggie quiche or baked omelet.

Pair with a high-protein smoothie for a hearty but convenient breakfast. We love this Green Vanilla Protein Smoothie or our Banana Blueberry Smoothie with protein powder for a dose of fruits in the morning.

FAQs for Healthy Apple Muffins

Can I make these gluten-free?

Yes, you can make this gluten-free if you use a cup-for-cup substitute gluten-free flour instead of the two wheat flours we call for. We do not recommend using almond flour or coconut flour for this recipe.

What is the best variety of apple to use for making apple muffins?

While Macintosh apples are best for applesauce, we do not recommend them for apple muffins because they will break down too much and get mushy. While you can use any firm snacking apple such as Braeburn, gala or Honeycrisp for quickbread and muffins, our favorite types of apples for muffins are golden apples.

moody blue patina background with a batch of apple muffins cooling on a baking rack

More Healthy Baking Recipes

If you’re looking for more fall baking recipes for snacks and breakfasts, try these ideas!

A loaf of pumpkin streusel bread, cut into slices and laid on a black patterned baking sheet

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Need more back-to-school snack ideas? Try this Peanut Butter Pretzel Energy Balls recipe or our np-bake Lemon Chia Snack Bars.

Thanks so much for reading. If you make these muffins please come back and leave a star rating and review.

Happy Cooking!

~Katie

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Healthy Apple Muffin Recipe {with Greek Yogurt}

★★★★★

5 from 3 reviews
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Description

These healthy Apple Muffins with Greek Yogurt are a nutritious breakfast or snack. Each one is filled with natural whole grains and has 5 grams of protein!

Ingredients

Scale

Streusel topping

  • ¼ cup old-fashioned oats
  • ¼ cup all-purpose flour
  • 2 tablespoons granulated natural cane sugar (evaporated cane juice)
  • 2 tablespoons unsalted butter, softened
  • ½ teaspoon cinnamon

Muffins

  • 1 large egg
  • ¾ cup plain Greek yogurt, preferably 0% fat
  • 2/3 cup granulated natural cane sugar (evaporated cane juice)
  • 1/4 cup avocado oil or organic canola oil
  • ¼ cup apple juice, apple cider or water
  • 1 cup all-purpose flour
  • 3/4 cup whole-wheat flour, preferably white whole-wheat
  • 2 teaspoons baking powder
  • 1 teaspoon cinnamon
  • ½ teaspoon baking soda
  • ½ teaspoon nutmeg
  • ½ teaspoon salt
  • 1 large apple, peeled and finely diced

Instructions

  1. Preheat oven to 375ºF. Coat a 12-well muffin tin with cooking spray or line with paper muffin liners.
  2. Rub together oats, ¼ cup all-purpose flour, 2 tablespoons cane sugar, butter and ½ teaspoon cinnamon with clean fingertips in a small bowl until crumbly.
  3. Whisk egg, yogurt, evaporated cane juice, oil and apple juice in a large bowl until smooth. Whisk 1 cup all-purpose flour, whole-wheat flour, baking powder, 1 teaspoon cinnamon, baking soda, nutmeg and salt in a medium bowl. Add the dry mixture to the wet mixture and stir to combine. Add the apple and stir to combine.
  4. Divide the batter among the prepared muffin tin wells. Top with the streusel, dividing evenly. Transfer to the oven and bake until a toothpick inserted in the center comes out clean, 26 to 28 minutes. Let cool in the pan 10 minutes before removing the muffins from the muffin tin, and transferring to a wire rack to cool.

Notes

Freezing and Reheating Instructions

  1. Keep at room temperature for two days in an airtight container.
  2. To freeze place the muffins in a freezer Ziplock bag and press the extra air out of the bag. Seal shut and freeze up to 1 month.

  3. Thaw at room temperature for 10 hours or up to 1 day.

  4. For the best texture, we recommend reheating the frozen and thawed muffins for 20 seconds in the microwave or in the oven (wrapped in foil) for 10 to 15 minutes at 350 degrees.

  • Prep Time: 30 minutes
  • Cook Time: 28 minutes
  • Category: Snack
  • Method: Baked
  • Cuisine: American

Nutrition

  • Serving Size: 1 muffin
  • Calories: 217
  • Sugar: 17 g
  • Sodium: 170 mg
  • Fat: 8 g
  • Saturated Fat: 2 g
  • Trans Fat: 0 g
  • Carbohydrates: 34 g
  • Fiber: 2 g
  • Protein: 5 g
  • Cholesterol: 22 mg

Keywords: apple streusel muffins, healthy apple muffin recipe, greek yogurt apple muffins,apple yogurt muffins, whole grain apple muffins

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