Whole Wheat Apple Crumb Muffins
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These soft and moist Whole Wheat Apple Crumb Muffins are filled with sweet apples and piled high with a brown sugar streusel topping! They are a healthier yet delicious fall treat perfect for breakfast or snacking. Plus they freeze beautifully and only take 10 minutes of hands-on time.
By the end of summer I always feel like I am just waiting for Fall to come. I want to break out the cinnamon and pumpkin and apple cider as soon as I can! Well, my friends, we’re finally here. And that means I have a new crazy delicious fall recipe for you to try.
These Whole Wheat Apple Crumb Muffins are SO good. The recipe is adapted from my recipe for The Best Blueberry Muffins, but I use whole wheat pastry flour instead. Don’t be fooled be the whole wheat – they may be healthier, but they taste amazing!
I also make them with oil to keep the inside soft and moist, then pile them with a slightly adapted buttery crumb topping (and who doesn’t love that?). Then I finish them off with a deliciously sweet vanilla icing, although they are just as yummy without the icing.
What is whole wheat pastry flour?
Instead of using regular whole wheat flour, I use whole wheat pastry flour in this recipe. Pastry flour has a lower protein content than regular flour, which makes baking products softer and more tender. Whenever you are baking muffins, cakes, or quick breads, pastry flour is a great option to create the perfect texture in your recipe.
Whole wheat pastry flour has the added benefit of retaining the bran and germ nutrients, so it is more nutritious, extra flavorful, and still results in soft, tender baked goods. It’s a fantastic way to bake with whole grains yet maintain the texture you’d get in a bakery muffin!
Ingredients for Whole Wheat Apple Crumb Muffins
- Whole wheat pastry flour – This is my flour of choice, but you can also use 1/2 whole wheat flour and 1/2 all-purpose flour, or you can use 100% whole wheat white flour.
- Dark brown sugar – Brown sugar adds extra moistness to the muffin. You will also use it or light brown sugar for the crumb topping.
- Baking powder
- Kosher Salt
- Cinnamon
- Nutmeg
- Oil – Vegetable oil makes the muffins very moist. If you want less fat content, you can also do half oil and half applesauce.
- Milk – I prefer to use whole milk for the extra fat content, but 1% or 2% also work well.
- Eggs
- Vanilla
- Apples – I used Honeycrisp, but there are other options. See the section about which apples work best below.
- Granulated sugar
- Butter – I prefer to use unsalted since I have added salt to the recipe already. Salted butter brands can vary on how much salt they add so I like to use unsalted so I can control the amount of salt. If you only have salted butter, than be sure to reduce or completely omit the salt called for in the recipe. The butter will be used in the crumb topping.
- Confectioners sugar
How to Make Whole Wheat Apple Crumb Muffins – Step by Step
Preheat and prepare pan. Preheat oven to 375oF. Line pan with paper muffin cups or grease the wells and top of pan with non-stick cooking spray.
Make crumb topping. In a small bowl, combine flour, salt, brown sugar, granulated sugar, and cinnamon. Work butter into mixture until crumbly. Set aside.
Combine dry ingredients. Whisk together the flour, brown sugar, baking powder, salt, and spices in a large bowl. Make a well in the center by pushing the dry ingredients to the side and creating a hole in the middle.
Combine wet ingredients. In a second mixing bowl, whisk together oil, milk, eggs, and vanilla extract.
Add wet to dry. Pour wet ingredients all at once into the well in the flour mixture. Mix quickly and lightly with a rubber spatula, but do not overmix. The batter will be lumpy.
Stir in apples. Be sure to not overmix at this point. Just a few good folds with the apples and you’re all set to scoop!
Scoop batter into the pans. Divide the batter into the wells, filling each well.
Sprinkle on crumb topping. I sprinkle on about a tablespoon or so onto each muffin. Just press lightly if needed.
Bake muffins. Bake for 25 minutes, or until golden and a toothpick inserted comes out clean. Allow to cool in the pan for 5 minutes, then transfer each muffin to a wire cooling rack to continue to cool.
Make icing. In a small mixing bowl, stir together all icing ingredients. Adjust consistency if needed. Drizzle of cooled muffins.
Recipe Tips
- Measure your flour accurately. The best method is to use a kitchen scale and measure your flour in grams. If you don’t have a scale, use a spoon to scoop the flour into the measuring cup, then level it off gently with a butter knife. For more details, read my post on How to Measure Flour Correctly.
- Don’t overmix the batter. Once you add the wet ingredients to the dry, mix until everything is just combined. Don’t worry if it is still lumpy. Overmixing can lead to tough muffins or cause tunneling, which is essentially large air pockets (holes) in the muffins. So no overmixing!
- Portion your muffins evenly. Nowadays they make awesome LARGE ice cream/cookie/muffin scoopers that are perfect for getting even sized muffins.
Recipe FAQ’s
I use honeycrisp apples in this recipe because they are sweet, juicy, and don’t break down too much while baking. They’re perfect!
Before there are other apple options that could work well too. Check out my post on The Best Apples for Baking to find the best substitutes.
No, you can make the muffins without liners if you prefer. Just make sure to grease the inside AND TOP of the muffin tin very well before baking. The muffins will bake up around the edges and stick to the top if it isn’t greased well.
You absolutely can if you want! Just be sure to measure by weight or if measuring by cups, then scoop the flour into your cup and level off. Don’t just dip the cup into your flour or pack it down, which can result in way too much flour!
I wouldn’t recommend using 100% regular whole wheat flour as they might come out very heavy and dense. Regular whole wheat flour has a much higher protein content so it can result in a heavy muffin.
If you don’t have whole wheat pastry flour on hand but want to still make these whole wheat I would recommend using white whole wheat flour, which has a softer texture. Or try using half whole wheat flour and half AP flour.
If your muffins turned out flat, it is likely because the leavening agent (baking powder) was ineffective of they were slightly underbaked. Check the expiration date of your baking powder (it doesn’t usually last past 6 months). Also make sure to bake until a toothpick inserted in the center of the muffin comes out clean.
You can read more about How to Make Muffins – Ultimate Guide.
Cool your muffins thoroughly, then store them in an air-tight container at room temperature for 3-5 days. If you want them to last longer, follow the freezing instructions below.
Yes, muffins are great for freezing! Cool thoroughly, then wrap individually in plastic wrap. Place the wrapped muffins in a zipper bag for an extra layer of protection from the cold. Then freeze for up to three months. Thaw at room temperature or using the defrost setting on the microwave.
More Recipes to Try
Whole Wheat Apple Crumb Muffins
Ingredients
Muffins
- 2¼ cups (270 g) whole wheat pastry flour
- 1 cup (213 g) (213g) packed light or dark brown sugar
- 1 tablespoon baking powder
- ¼ teaspoon kosher salt
- 2 teaspoons ground cinnamon
- ¼ teaspoons ground nutmeg
- ⅔ cup (160 mL) vegetable oil
- ½ cup + 2 tbsp (142 mL) milk
- 2 large eggs room temperature
- 1½ teaspoon vanilla extract
- 1½ cups peeled, chopped apples about 2 medium apples
Crumb Topping
- ½ cup (48 g) whole wheat pastry flour
- 1/8 teaspoon kosher salt
- ¼ cup (53 g) (53 g) packed light or dark brown sugar
- 2 tablespoons granulated sugar
- ½ teaspoon ground cinnamon
- ¼ cup (1/2 stick, 57 g) unsalted butter melted
Vanilla Icing (optional)
- 1 cup (120 g) confectioners sugar
- 2-3 tablespoons milk or heavy cream
- ½ teaspoons ground cinnamon
- ½ teaspoon vanilla extract
Instructions
- Preheat and prepare pan. Preheat oven to 375oF. Line pan with paper muffin cups or grease the wells and top of pan with non-stick cooking spray.
- Make crumb topping. In a small bowl, combine flour, salt, brown sugar, granulated sugar and cinnamon. Work butter into mixture until crumbly. Set aside.
- Combine dry ingredients. Whisk together the flour, brown sugar, baking powder, salt, and spices in a large bowl. Make a well in the center by pushing the dry ingredients to the side and creating a hole in the middle.
- Combine wet ingredients. In a second mixing bowl, whisk together oil, milk, eggs, and vanilla extract.
- Add wet to dry. Pour wet ingredients all at once into the well in the flour mixture. Mix quickly and lightly with a rubber spatula, but do not overbeat. The batter will be lumpy. Stir in apples. Divide the batter into the wells, filling each well.
- Sprinkle on crumb topping.
- Bake muffins. Bake for 25 minutes, or until golden and a toothpick inserted comes out clean. Allow to cool in the pan for 5 minutes, then transfer each muffin to a wire cooling rack to continue to cool.
- Make icing. In a small mixing bowl, stir together all icing ingredients. Adjust consistency if needed. Drizzle on cooled muffins.
Notes
- Measure your flour accurately. The best method is to use a kitchen scale and measure your flour in grams. If you don’t have a scale, use a spoon to scoop the flour into the measuring cup, then level it off gently with a butter knife. For more details, read my post on How to Measure Flour Correctly.
- Don’t overmix the batter. Once you add the wet ingredients to the dry, mix until everything is just combined. Don’t worry if it is still lumpy. Overmixing can lead to tough muffins or cause tunneling, which is essentially large air pockets (holes) in the muffins. So no overmixing!
- Portion your muffins evenly. Nowadays they make awesome LARGE ice cream/cookie/muffin scoopers that are perfect for getting even sized muffins.
- Storage: Cool, then store in air-tight container at room temperature for 3-5 days.
- Freezing: Cool, then wrap individually in plastic wrap. Store in a zipper bag and freeze for up to 3 months. Thaw at room temperature or in the microwave with the gentle defrost setting.
- For less fat content: You can use half oil and half applesauce for less fat.
- Best Apples: I use honeycrisp apples in this recipe because they are sweet, juicy, and don’t break down too much while baking. They’re perfect! But there are other apple options that could work well too. Check out my post on The Best Apples for Baking to find the best substitutes.
- No liners? You can make the muffins without liners if you prefer. Just make sure to grease the inside AND TOP of the muffin tin very well before baking. The muffins will bake up around the edges and stick to to the top if it isn’t greased well.
- Flour substitution: You can use AP flour if you want for these muffins. I wouldn’t recommend using 100% regular whole wheat flour as they might come out very heavy and dense. Regular whole wheat flour has a much higher protein content so it can result in a heavy muffin. If you don’t have whole wheat pastry flour on hand but want to still make these whole wheat I would recommend using white whole wheat flour, which has a softer texture. Or try using half whole wheat flour and half AP flour.
Apple muffins have always been my favorite growing up! I’m glad to have found your recipe. I will definitely be trying it. Thank you!
Such a nice cozy, homey feeling.
My family loves when I make these apple crumb muffins! They’re the perfect grab and go breakfasts and they never last long on the table. Definitely need to start making a bigger batch!
Exactly! Thank you
The best fall breakfast! I made a double batch so we would have plenty to freeze for easy breakfasts and snacks! They are so good with the crumb topping!
Excellent! thank you Amy
I am drooling over these muffins!! I am so ready for apple season, so I know these muffins will be made on repeat in my house 🙂
🙂 I hope they turn out well for you 🙂
I have never made anything like this before and I am really tempted to make these tomorrow! I love how simple and cute these look. Thank you for sharing this recipe, I cant wait to give these a go!
I hope it turns out well for you 🙂
These whole wheat apple crumb muffins taste like a sunny crisp Fall day! Love them in the morning or even as a dessert!
Thanks for your sweet feedback! I make these all the time in fall, too 😀
This is a great snack to have with my coffee! I may have to double the Apple Muffins recipe to hide them from my family!
I’m glad that everyone loves them so much!
Great Fall Flavors in these nutritious and delicious muffins!
Thank you Julie!
Oh these muffins are addicting! The perfect way to start off a day … and the crumb topping is to die for!
Yay I am so glad you love them as much as I do, Patty! And YES it is all about that crumb 😀
These apple muffins were perfectly moist, fluffy and had all the flavors of fall. Thanks for this recipe, I’ll be making another batch of these soon 🙂
Thanks for your sweet feedback, Kathryn! I make these nonstop in fall, too 😀
Your crumb topping for this Whole wheat apple muffin recipe is the BEST! This recipe is definitely a keeper!
Thanks so much, Leslie 😀 I really appreciate your sweet comment and am so happy you enjoyed!
These muffins were the perfect way to get our day started. Paired so well with our coffee!
Thanks for your sweet comment, Marta! I’m so glad they helped put a little yummy pep in your morning step 🙂
I love any dessert recipe that has a crumble top! These muffins are beyond delicious. Can’t wait to try them over the weekend.
The crumb really takes them to the next level! I hope you enjoy 🙂
These are scrumptious and I am going to warn you kind of addicting. Made some on Sunday for the family and they have been gobbled all up!
That makes me so happy to hear, Beth! Thank you for sharing your sweet feedback!
Wow, what a perfect fall dessert! These muffins look so delicious, will be perfect with a cup of tea.
Oh yes, there is nothing like snuggling up with a warm muffin and a mug of tea! Hope you enjoy 🙂
These were perfect for the kiddos! Thanks for a wonderful recipe!
I am so glad they liked them, Kristen!
A batch of these would not last long in our home! I go weak in the knees when faced with a crumb topping and I would have a hard time sharing a batch of these! Such a fantastic recipe – thank you for it!
Same here, Sashi! It’s always fun writing how long leftovers will keep well for a recipe like this, because I know they’ll be going fast! Thanks for your comment 🙂
These muffins are so sweet and delicious. I love that it is made with whole wheat too!
I’m so happy you enjoyed, Sharon! Whole wheat is definitely my favorite for that deep, earthy flavor!
Did not even know that whole wheat pastry flour was a thing?! This is a serious game changer. Thanks for sharing this recipe!
Yes it’s the best of both worlds!! You’re welcome Brittany 🙂