Made with whole wheat flour and just two tablespoons of oil, these healthy apple muffins are a perfect snack or breakfast.

Healthy apple muffins in a basket with a blue checkered towel.

My kids are muffin monsters. They love muffins, most any kind, but especially Grandma’s muffins! She’s the undisputed muffin queen. In fact, when I said I was making healthy apple muffins for this post, they said, in a nice way of course, that maybe Grandma should be making them.

Okay, my feelings aren’t hurt. I learned my love of baking from my mom.

One of my goals is to look for healthier alternatives to the high fat, loaded with sugar products offered in bakeries, coffee shops, and grocery stores. I’ve developed several muffin and quick bread recipes that cut back drastically on the fat and sugar content of baked goods. Instead I include good for you ingredients like fruit, applesauce, whole wheat flour, bran, and so on.

These healthy apple muffins made with whole wheat flour, applesauce, and grated apples are full of flavor, totally satisfying, and they’re good for you, too.  With only 145 calories each, compared to a Panera muffin at 450 calories, I think you’ll agree that homemade is better.

Apple muffins made with whole wheat flour in a silver muffin pan.

About these healthy apple muffins:

I like to shred the apples for apple muffins. You can leave the peeling on the apple and the shredded apple provides lots of flavor and moisture. My son, who is quick to spot discernible chunks of fruit, gives his approval to these muffins.

I use a mixture of applesauce (those little individual sized cups are exactly 1/2 cup which works perfectly in this recipe), milk, and just 2 tablespoons of canola oil. Added to whole wheat flour, baking powder, a dash of salt, and spiced with cinnamon and nutmeg, these muffins couldn’t be easier to stir up.

Use the one bowl method: Stir together the wet ingredients in a large bowl and measure the dry ingredients, placing them right on top. Lightly stir the dry ingredients with your finger (or a dry spoon) and then gently stir it all together. Don’t over mix, the ingredients just have to be combined. 

Fill your muffin cups and bake for 20 minutes. Nothing to it! 

Overhead view of apple cinnamon muffins in a muffin tin.

Making healthy apple muffins your own:

If you’d like to change things up a bit, I have a few ideas for you.

  • Add chopped nuts. My kids have nut allergies so I stay away from nuts, but 1/2 cup of lightly toasted walnuts would be so tasty.
  • Add raisins or chocolate chips – a 1/2 cup of these would be perfect, too. 
  • Use regular all-purpose flour instead of all or part of the whole wheat flour. My family is accustomed to the heartier flavor and texture of whole wheat but if you’re welcome to make these with white flour. 
  • Sprinkle cinnamon sugar or coarse sugar on the tops of the muffins before baking. Or make a streusel topping. Another idea: brush the tops of the baked muffins with cinnamon flavored simple syrup.
  • Instead of shredding the apple, dice it finely. 

Whole wheat apple muffins in a metal basket with a blue and white checkered towel.

Can I freeze these muffins?

Yes! I love to make a big batch of muffins and freeze them in individual bags for up to 3 months, ready to put into lunch boxes. They’ll thaw out by lunch time. Or warm a frozen muffin in the microwave for a quick snack.

Is there a muffin monster in your home?

Appease the monster with more delectable muffins! Try:


Healthy whole wheat apple cinnamon muffins in a muffin pan.

A bit of nostalgia…

We updated this recipe and post with more valuable information (and pictures!) in January, 2020. However, this recipe was my very first post way back in February 2011, shortly after my first child was born. It was called “Rachel’s Recipe Reviews” back then! What started as a creative outlet (“hobby”)  to fill long hours at home with a newborn turned into a career that I absolutely fell in love with. Because I’m too sentimental to delete those very first words that I typed, I’ll include this first paragraph written as a new food blogger:

“One of my favorite things to do is cook and bake. Now that I am a stay at home mom, I have more time to invest into this love of mine. I have tons of great cookbooks, many of which I didn’t use often. It wasn’t because they were not good cookbooks, but more because I had a few go-to recipes that I didn’t stray far from. That is obviously boring and not fun at all! It is my goal to draw from these cookbooks to create some really fantastic recipes. I love to talk with fellow “foodies” about what I have made and what I did to make it better (to mine and my husband’s palates). I am hoping that my mother won’t be the only one that will read and benefit from this blog. I am also hoping that I can stick with it. Enough talk, here is my first recipe!”

Now, with millions of readers each month, it’s definitely more than just a hobby. I’m so glad I wrote that first post!

Healthy apple muffins in a basket with a blue checkered towel.

Apple Cinnamon Muffins

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 20 minutes
Total Time: 30 minutes

Easy Apple Cinnamon Muffins — a healthy and delicious breakfast or snack!


  • 3/4 cup milk
  • 1/2 cup unsweetened applesauce
  • 1 large egg
  • 2 tablespoons canola oil
  • 2 cups whole wheat flour
  • ½ cup sugar
  • 2 teaspoons baking powder
  • 1/2 teaspoon salt
  • 1 teaspoon cinnamon
  • ¼ teaspoon nutmeg
  • 1 heaping cup shredded Granny Smith apples, unpeeled (other varieties will work as well)


  1. Heat oven to 400ºF. Prepare muffin tins by spraying with cooking spray or line with paper baking cups.
  2. In large bowl, stir milk, applesauce, egg and oil, with fork or wire whisk until well mixed. Fold in apples.
  3. Stir in flour, sugar, baking powder, cinnamon, nutmeg, salt, all at once just until flour is moistened (batter will be lumpy). Divide batter evenly among muffin cups. 
  4. If desired, sprinkle tops of muffins with cinnamon sugar or coarse sugar. 
  5. Bake 20 minutes or until golden brown. Let stand about 5 minutes in pan, then remove from pan to wire rack; if baked in paper baking cups, immediately remove from pan to wire rack. Serve warm or room temperature.


  • If preferred, all-purpose white flour can be substituted for all or part of the whole wheat flour.
  • Any variety of apple would work well. If desired, apple can be finely diced instead of shredded.
  • There is 1/2 cup of applesauce in individual sized serving cups.
Nutrition Information:
Yield: 12 Serving Size: 1 muffin
Amount Per Serving: Calories: 145Total Fat: 4gSaturated Fat: 1gTrans Fat: 0gUnsaturated Fat: 3gCholesterol: 17mgSodium: 184mgCarbohydrates: 26gFiber: 3gSugar: 10gProtein: 4g sometimes provides nutritional information, but these figures should be considered estimates, as they are not calculated by a registered dietitian. Please consult a medical professional for any specific nutrition, diet, or allergy advice.

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