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Whole Wheat Apple Muffins

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Easy whole wheat apple muffins are a great grab and go fall breakfast option. These muffins are nut free, egg free, and freezer friendly!

Easy whole wheat apple muffins are a great grab and go fall breakfast option. These muffins are nut free, egg free, and freezer friendly! #howtomake #freezerfriendly #muffins #fallbaking #breakfastideas #mealprep #backtoschool

A friend of mine messaged me a few weeks ago to ask if I had a good apple muffin recipe, because her tree is producing a lot of apples this year, but she hadn’t yet found an apple muffin recipe with enough apple to suit her tastes, and was hoping I’d have a different option for her to try. I did not, but I do now!

I’d like to start off by saying that my daughter calls these cupcakes, so that makes me happy, and affirms my belief that they are indeed, delicious, and a recipe you all may enjoy. I’m always extra critical of my “healthier” baked goods recipes because I honestly don’t see the point in having a “healthier” option that doesn’t satisfy your sweet tooth craving and leaves you wanting the real thing.

Whole wheat apple muffins make a great easy weekday breakfast!

Fall always means a return to structure. Whether we are sending kids back to school or just planning out how to finish the year strong, there’s lots to do! So this is also the season where I bake a lot of muffins. These whole wheat apple muffins are a favorite (especially with fresh picked apples!). Other recipes we enjoy include these banana chai muffins or for a treat, some mini Nutella doughnut muffins.

Why use whole wheat flour?

I make these muffins with whole wheat flour to increase the fiber. If a muffin ends up being breakfast, it has to satisfy for at least a few hours. If you aren’t sure if you’ll love the flavor of the whole wheat flour, feel free to make a 50/50 split between whole wheat and white flour. The muffins are forgiving enough that the recipe will still turn out.

To keep the muffins looking lighter, I use a white whole wheat flour. I feel like this provides a finer texture, although it may be strictly a psychological thing.

What type of apples should I use?

The best apples to use to make apple muffins are the ones you have on hand. I’ve used several different kinds, mostly of the slightly sweeter and crisp variety. What you want to avoid is using a softer apple that will disintegrate during baking. Any apple with a nice firm texture works well. Think along the lines of honeycrisp, gala, macintosh, pink lady, etc.

beautiful apple photography by Goodie Godmother. All Rights Reserved.

No matter what your season in life looks like right now, I hope you lean in. Embrace the transitions, see the beauty in the chaos, grow. And I hope this apple muffin recipe makes at least the mornings a little sweeter. 😉

Happy baking, darlings!

Whole Wheat Apple Muffins

Whole Wheat Apple Muffins

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 25 minutes
Total Time: 35 minutes

These delicious whole wheat apple muffins are egg free, and make a great grab and go satisfying fall breakfast treat!


  • 2 1/2 cups white whole wheat flour
  • 3/4 cups brown sugar
  • 3/4 teaspoon salt
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1 1/2 teaspoons cinnamon
  • 1/4 teaspoon nutmeg
  • 1 teaspoon vanilla extract
  • 1/3 cup neutral oil **or** applesauce
  • 1 1/2 cups milk
  • 1 1/2 cups chopped fresh apple
  • turbinado sugar for topping (optional)


  1. Preheat the oven to 375 F and line 12 muffin tins with liners. Set aside.
  2. Stir together the dry ingredients in a large mixing bowl or the bowl of a stand mixer fitted with a paddle attachment. Whisk or stir until just combined... now you don't have to sift!
  3. In a separate bowl, whisk together the wet ingredients.
  4. Pour the wet ingredients into the dry, stirring slowly to incorporate. If using a mixer, run on low speed while you pour in your wet ingredients. Stop stirring as soon as the dry mixture is incorporated.
  5. Fold in the diced apple.
  6. Divide the batter evenly between the muffin wells, and top with turbinado sugar if desired.
  7. Bake 20-25 minutes until a tester inserted in a center muffin comes out clean, or when the top of the muffin springs back when touched. Be careful not to over-bake.
  8. Allow to cool on a wire rack before storing. The muffins will keep loosely covered at room temperature 2 days, or they freeze very well up to 2 months.


To make a lower fat muffin, substitute unsweetened applesauce for the oil.

You may also substitute buttermilk OR your favorite non-dairy milk for the milk in the recipe. If you use a non-dairy milk, the muffins are vegan. The only change is that the final texture may be a little less moist, and leftover muffins might not last as long.

Easy whole wheat apple muffins are a great grab and go fall breakfast option. These muffins are nut free, egg free, and freezer friendly! #howtomake #freezerfriendly #muffins #fallbaking #breakfastideas #mealprep #backtoschool


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  • Reply
    Nicole @Little Blog on the Homestead
    October 8, 2015 at 10:37 pm

    Mmm apples!! I absolutely love apple muffins better than anything else can’t wait to try this recipe.

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