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Healthy Apple Muffins Recipe (30 minutes!)

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Wait until you try this recipe for apple muffins! This easy apple muffins recipe takes just 30 minutes to make (plus a little time to cool!) and is made with basic ingredients you probably already have. My healthy apple muffins recipe is made with Pazazz apples, whole grains, cinnamon, and is sweetened with maple syrup, similar to my apple oatmeal bars, but in muffin form. Similar to my mini zucchini chocolate chip muffins, and mini blueberry muffins, these are the perfect blend of nutritious AND delicious!

Serve up this whole wheat apple muffins recipe for breakfasts, lunches, snacks, or even dessert. These healthy apple cinnamon muffins have just 150 calories, but pack in fiber and protein thanks to the whole grains, milk and eggs, and apples. They are a must for apple season and will make your house smell SO good.

And if you love apples, be sure to try my Instant Pot applesauce, caramel apple nachos, apple monkey bread, and peanut butter apple dip next.

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I’m so excited to partner with Pazazz apples to bring you this recipe for apple muffins that’s both nutritious and delicious! (sponsored) Apples are a year-round staple for us for meals, snacking, AND baking. And let me tell you, you’re going to want to get your hands on the Pazazz variety. Created right here in Minnesota, this apple is a cross between Honeycrisp and mystery pollinator and it’s the perfect blend of sweet, tart, and crunchy.

Let’s talk a little about apple nutrition. We all know the saying, “An apple a day…” but do we know WHY? It’s because apples are a sweet little package of fiber (4.5 grams per medium), prebiotics, antioxidants, and vitamin C!!!

Apples are an easy way to add nutrition into your day and this recipe for apple muffins is a delicious and nutritious way to start off your day. I go into more details below, but there are options for reducing the sugar even further or making them 100% whole grain, BUT, as written, they are light and fluffy bakery-style muffins with a delicious sweet and crunch streusel topping. It’s a small amount of sugar that gives the best apple muffins major sweet flavor.

Healthy apple muffins on baking rack

Estimated reading time: 10 minutes

Apple Muffins Video

What You’ll Love About This Easy Apple Muffin Recipe

  • Cozy apple and cinnamon flavors
  • Light and fluffy texture like a bakery muffin
  • Made with healthy ingredients
  • An easy prep-ahead breakfast or snack

Ingredients to Make Healthy Apple Muffins

This recipe for apple muffins is made from simple and wholesome ingredients:

  • Wheat germ – This helps to add an extra boost of protein and fiber to the muffins.
  • Milk – Use any milk variety. Cows milk, almond milk, oat milk, etc.
  • Apples – Pazazz apples work well here, but the most important thing is that they are fresh apples
  • Butter – Use your favorite variety of butter.
  • Oats – Use old fashioned oats, but not instant or steel cut oats.
  • Brown sugar – You can also use turbinado sugar for more texture, coconut sugar, or omit entirely, see below for tips.
  • All-purpose flour- Use all purpose or white whole wheat flour.
  • Whole grain flour – You can also use all all-purpose flour, white whole wheat flour, or oat flour.
  • Spices – Cinnamon, baking powder, baking soda, sea salt
  • Egg – Use your favorite type of eggs.
  • Maple syrup – Use pure maple syrup for best flavor.
  • Vanilla extract – Use high quality vanilla for best flavor.
Ingredients to make recipe for apple muffins

How to Make Healthy Apple Muffins Recipe

When I say these muffins are easy, I mean it! This healthy apple muffins recipe is ready in 30 minutes + a little time for them to cool. Here’s how we make them:

  • Prep ingredients. Preheat oven to 375 degrees Fahrenheit. In a medium bowl, mix together wheat germ and milk. Dice apples, you want them small, almost like a grated apple. In a small bowl, mix together streusel topping. Line muffin tin with paper liners.
Bowl of diced Pazazz apples
  • Mix dry ingredients for apple muffins. In a large bowl, mix together flours, cinnamon, baking powder, baking soda, and salt.
  • Whisk in wet ingredients. Add egg, maple syrup, and vanilla into the milk and wheat germ. Whisk until combined. Stir in dry ingredients until muffin batter is combined and fold in diced apples.
Bowl with easy apple muffins ingredients
  • Prepare muffins. Divide divide batter to lined muffin pan and sprinkle the streusel topping over the tops of the muffins.
  • Bake. Bake muffins until a toothpick inserted into the muffin comes out clean.

Frequently Asked Questions

Are apple muffins suitable for babies?

Yes, you can serve these cinnamon apple muffins to young eaters! Make sure that the apples are cut up into very small pieces and you can omit the brown sugar and white flour if you wish. (Full details on that below.)

Are apple muffins healthy?

You know I hate this question!!!! I kid, I kid. Yes, these simple whole wheat apple muffins contain a number of macro and micro nutrients that are important for healthy bodies. Between the apples, wheat germ, and whole grains, these muffins are healthy enough for breakfast – but they don’t taste like dense “healthy” muffins.

The full nutrition stats are below the recipe card. Each muffin has 146 calories, 3 grams fiber, and 5 grams protein.

Can you make this recipe for apple muffins without sugar?

You can use less sugar in these healthy apple spice muffins, see below for instructions.

Whole wheat apple muffins recipe with pat of butter on parchment paper

Storage Instructions

Store cooled muffins in an airtight container at room temperature for 2-3 days.

How to reheat

Let the whole wheat apple cinnamon muffins thaw at room temperature or reheat gently in the microwave before serving.

Can you freeze apple muffins?

Yes, you can freeze apple muffins in a freezer bag (like a stasher bag) for 2-3 months.

How to Serve Whole Wheat Apple Muffins to the Whole Family

I get it, feeding kids can be tough! But following the Division of Responsibility and knowing your job and your child’s job makes it SO much more enjoyable. You’ll be able to feed your kids any meal, which will help ensure that they are eating a variety of nutritious foods – with plenty of play food sprinkled in. 😉

Serve a small piece of the cinnamon apple muffins to your kiddos if you aren’t sure they will eat it and if you’re serving it as a meal, be sure to serve it with a few other items (see below for list).

All of my articles on feeding kids can be found here and if you want a FULL list of all of the videos I have with hacks, tips, scripts, and ideas for feeding kids, check out my instagram or tiktok page.

Whole wheat apple muffins on cooling rack

Substitutes + Nutrition

If you want to swap out any of the ingredients and toppings, here are a few ways you can add even more nutrition into this meal:

These healthy apple spice muffins are low in sugar naturally, but here are a few ingredient swap ideas for you:

  • Sugarfree – If you’re making these apple muffins for toddlers and don’t want the extra sugar, you can omit the brown sugar on the top and you could swap out the maple syrup for applesauce for a refined sugar free. (Check labels on applesauce if you feel really strongly about sugar, I recently brought home applesauce with high fructose corn syrup!)
  • 100% Whole Grain – The blend of wheat germ, whole wheat flour, and all-purpose flour gives these muffins great lift and flavor (aka they aren’t too dense), but if you want them to be 100% whole grain, swap out the all-purpose flour for white whole wheat flour or whole wheat flour. (They may be a bit denser.)
  • Dairy-Free – You can use a milk alternative and a dairy-free butter for the topping.
Healthy apple cinnamon muffin with pat of butter

What to Serve with Easy Apple Muffins Recipe

You can find the full nutrition facts below the recipe card, but while these muffins are nutritious, they are not filling enough for a full meal!

This easy apple muffins recipe covers your fruit and grain portion of the meal, but pair them with a protein like creamy scrambled eggs, breakfast sausage, hard boiled eggs, a slather of peanut butter, almond butter, a sprinkle of chia seeds, or a cup of milk to turn it into a satisfying meal. Don’t forget a cup of cold foam coffee!

More Healthy Apple Recipes

If you like this recipe for apple muffins, you might also like some of these other easy and healthy apple recipes:

Helpful Tools to Make Whole Wheat Apple Muffins Recipe

  • Stasher Bags – Store the simple healthy apple muffins in stasher bags – perfect for pantry or freezer.
  • Wheat Germ – Don’t forget healthy wheat germ! This gives the muffins extra fiber and protein. Use extra in granola or in baked goods.
  • Silicone Spatula Set – These spatulas actually stay clean, no staining.

It’s 5pm. Are you still wondering what’s for dinner?

Menu Plans by My Everyday Table can help you out.

The plan addresses three major issues when it comes to weeknight dinners: having a plan, time, and one family meal

You’ll save time, save money, waste less food, and feel calm when 5pm hits because your dinner is already planned.


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Healthy apple muffins on baking rack

Healthy Apple Muffins Recipe

  • Author: Emily Dingmann of myeverydaytable.com
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 minutes
  • Yield: 12 muffins 1x
  • Category: Breakfast
  • Method: Bake
  • Cuisine: American
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This healthy whole wheat apple muffins recipe makes a great breakfast, lunch, or snack! Make this recipe for apple muffins in just 30 min.


  • 1 cup wheat germ
  • 1 cup milk
  • 2 Pazazz apples (about 2 cups diced)
  • 1 Tbsp. cold unsalted butter cut into small pieces
  • 1 Tbsp. old-fashioned oats
  • 2 Tbsp. brown sugar
  • 1/2 cup all-purpose flour
  • 1/2 cup whole wheat flour
  • 1 Tbsp. cinnamon
  • 1 tsp. baking powder
  • 1 tsp. baking soda
  • 1/4 tsp. salt
  • 1 egg
  • 1/3 cup maple syrup
  • 1 tsp. vanilla extract


  1. Preheat oven to 375 degrees F.

  2. Stir together wheat germ and milk in a large bowl and set aside. 

  3. Dice apples. (You want them to be pretty small.)

  4. Make crumb topping. In a small bowl, mix together butter, oats, and brown sugar with a fork. 

  5. In a medium bowl, stir together all-purpose flour, whole wheat flour, cinnamon, baking powder, baking soda, and salt with a fork. 

  6. Whisk the egg, maple syrup, and vanilla into the wheat germ bowl. Stir in dry ingredients and mix until combined. Fold in diced apples and transfer batter to lined muffin tins. Top muffins with crumble topping. Divide mix (about 1/3 cup scoop) into muffin tins, they should full. 

  7. Bake for about 15-20 minutes, or until a toothpick inserted in the middle of a muffin comes out clean.


  • See above for ingredient substitutions. 

Keywords: whole wheat apple muffins recipe, recipe for apple muffins, healthy apple muffins recipe, easy apple muffins recipe

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healthy apple muffins on cooling rack

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  1. Donna

    Made these last night. I didnt have apples, substituted 2 cups worth of shredded carrots, raisins and pecans. I confess I did add just a little white sugar to the batter and made double sprinkle for the top.
    Other than that I followed the recipe. I think soaking the wheat germ in the milk made a big difference between this and other similar recipes I have tried.
    They are awesome! Thank you.