Healthy Apple Muffins
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!
Table of contents
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
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.
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
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.
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.
Yes! Simply swap out the Greek yogurt and use the same amount of applesauce. Either using purchased or follow our easy applesauce recipe. Just don’t add any sweetener to it! Then use your favorite non-dairy butter, such as Earth Balance. Note that the streusel will be a little darker.
More Healthy Baking Recipes
If you’re looking for more fall baking recipes for snacks and breakfasts, try these ideas!
- This honey, date and raisin-sweetened Healthy Zucchini Oat Bread is sturdy enough for a lunchbox and rich in fiber.
- If you haven’t tried baking with spelt flour before, these Whole Grain Banana Muffins are a great place to start.
- My kiddos love it when I bake a loaf of this Healthy Pumpkin Bread with Chocolate Chips. And it always disappears too fast!
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}
- Total Time: 58 minutes
- Yield: 12 1x
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
Streusel topping
- 1/4 cup old-fashioned oats
- 1/4 cup all-purpose flour
- 2 tablespoons granulated natural cane sugar (evaporated cane juice)
- 2 tablespoons unsalted butter, softened
- 1/2 teaspoon cinnamon
Muffins
- 1 large egg
- 3/4 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
- 1/4 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
- 1/2 teaspoon baking soda
- 1/2 teaspoon nutmeg
- 1/2 teaspoon salt
- 1 large apple, peeled and finely diced
Instructions
- 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 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.
Notes
Freezing and Reheating Instructions
- Keep at room temperature for two days in an airtight container.
- 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.
- Thaw at room temperature for 10 hours or up to 1 day.
- 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
These are SO good! I wanted to bake some muffins that were healthier than the typical recipes, so I immediately thought of your site and did a search. This recipe caught my eye because it sounded like the perfect one for Fall weather, and it did not disappoint. The crumb was so tender, and we loved the apple/cinnamon flavors and streusel topping. Great recipe!
Thank you for coming back to report on how the apple muffins came out, Bernadette. I am happy to hear you liked them! Please let me know what you try next.
I searched many apple and cinnamon muffin recipes and chose this one for its yogurt and cider ingredients and the photo looked so yummy. I am not a fan of a lot of topping on muffins so just sprinkled them with turbinado and cinnamon mixture. They have a great flavour but we found them very dry. I used Honeycrisp apples and I think they would be better using maple syrup for moisture rather than sugar.
Thanks so much! Let me know if you do try it. I tested the recipe with maple (as that’s my preferred sweetener) and had issues with them not rising properly and they were quite dark. The dome was much better with the granulated sweetener.
I made them today and even my mom who is not fan of sweets – was surprised of how good these muffins are!
Thank you for the amazing (and underrated) recipe, it will be my “go to” this fall:)
These are the perfect fall muffin – love all the apple!
So tempting with that yummy streusel!! Perfect treat to start the day!
They look really good!
Thanks so much. Hope you enjoy them!
These look so tasty, apple and cinnamon are such a great combination. These are perfect for lunchboxes!
Thank you so much Hope. You really can’t go wrong with apple and cinnamon.
There is nothing to be “shad” about as long as these beauties are around. They look absolutely scrumptious and I am wishing I had that whole plate sitting right in front of me. Come to think of it. . .it’s been waaaay too long since I’ve sunk my teeth into a muffin. . .so yeah. . .I’m way overdo for these little treats. Loving the inclusion of Greek yogurt.
That’s the spirit! Ha ha. Thanks so much Lynn and for stopping by.
These look lovely, what a great snack to have on hand when you’re at work or school
Thanks so much Amy! That was my thought too! Now our freezer is stocked with them (after all those tests!) Thankfully the girls aren’t sick of them at all. My little one had one defrosted for breakfast this morning in fact.
I love to bake with buttermilk and yogurt, it results in such a tender crumb, love these!
Same here Sue. It really is a great way to add texture and flavor without adding a ton of calories from fat or sugar.
That crumbly topping looks amazing!
Why thank you Sandi. Have a great day.
These muffins look amazing! I’ll definitely be baking up a batch for our back-to-school mornings this week!
Really? That is awesome Martha. I hope you had a great summer.
I can’t resist anything with streusel! These apple muffins look excellent and are a perfect treat to welcome Fall!
I really can’t resist streusel either. I much prefer a streusel topped pie to a double crust any day.