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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. Serve up this whole wheat apple muffins recipe for breakfasts, lunches, snacks, or even dessert. They have just 150 calories, but pack in fiber and protein thanks to the whole grains, milk and eggs, and apples…

Healthy apple muffins on baking rack

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!!!

Bowl of diced Pazazz apples

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 muffins major sweet flavor.

recipe for healthy apple muffins

How to Make Healthy Apple Muffins:

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. Mix together wheat germ and milk. Dice apples. Make streusel topping.
Ingredients to make recipe for apple muffins
  • Mix dry ingredients for apple muffins. In a medium 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 combined.
Mixing bowl with whole grain muffin batter and chopped apples
  • Divide. Transfer healthy apple muffins batter to lined muffin tins and top with crumble topping.
  • Bake. Bake muffins for 15-20 minutes, until a toothpick inserted into the muffin comes out clean.

Recipe for Apple Muffins FAQs:

Are apple muffins suitable for babies?

Yes, you can serve these 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 apple muffins be frozen?

Yes, read below for freezing instructions.

Easy apple muffins on cooling rack

How to Store Leftover Muffins:

Store the muffins in an airtight container at room temperature for 2-3 days, or store in a freezer bag (like a stasher bag) for 2-3 months.

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

Easy Apple Muffins Recipe Nutrition + Substitutes:

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

  • Less Sugar – 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. (Check labels on applesauce, I recently (accidentally) 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.
Whole wheat apple muffins on cooling rack

More Easy 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:

  • 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.
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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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