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Whole Wheat Apple Muffins

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Whole wheat apple muffins are hearty and fluffy with hints of sweet baked apples. This is a simple muffin made from whole wheat flour, honey, cinnamon, eggs, milk, and oil. Everything is mixed together to form a batter, then baked in muffin cups until golden brown.

Serve as a quick and healthy breakfast, or as healthy snacks with tea, coffee or a smoothie. If you love muffins like we do, then you might also want to try our popular Baked oatmeal breakfast cups with six delicious flavors or our rhubarb whole wheat muffins which have a sweet and tart taste.

Whole wheat apple muffins piled into a bowl lined with a linen kitchen towel.

Healthy Apple Muffins

  • These muffins can be put together fast using wholesome ingredients you probably already have in your kitchen.
  • Whole wheat flour gives these muffins a heartier texture, but can easily be swapped with all-purpose flour if desired.
  • This is the perfect recipe to make with in-season ripe crisp apples. Feel free to use your favorite apple variety.
  • These can be baked in 20 minutes. Just dump ingredients into a bowl with chopped apples (or grated apple), add batter to a muffin pan and bake.
  • Make a double batch and store extra in the freezer!
  • We love muffins and have many muffin recipes including our easy oatmeal muffins with six flavors and delicious blueberry yogurt oat muffins.
Recipe ingredients on a counter including bowls of milk, flour, oil, cinnamon, honey, baking soda and two apples.

Recipe Ingredients

APPLES: Many people enjoy granny smith apples with baking muffins because of their tart flavor (they taste delicious combined with the sweetness from the muffin). I used pink lady apples which are crisp and tangy sweet. Other fresh apples that can also be used including fuji, gala and honey gold. There’s no need to peel the apples before adding them to the recipe. The skin can be left on.

Want more apple recipes? Try our easy and delicious apple crisp or our easy applesauce cookies.

DRY INGREDIENTS: Whole wheat pastry flour (or regular whole wheat flour) is mixed with cinnamon, baking powder, baking soda, and salt. If preferred, divide the flour using 1 cup whole wheat flour and ¾ cups white all-purpose flour.

WET INGREDIENTS: Milk, vegetable oil, and one egg are mixed in with the dry ingredients. This recipe can be made with dairy-free milk such as almond milk, oat milk, soy milk etc. You can also substitute the oil for olive oil, coconut oil, avocado oil or melted butter.

VARIATIONS: Substitute half of the apples with a different apple style for variation. Or use 1 cup apples and 1 cup fruit or dried fruit (raisins, chopped apricots etc.) Try adding chopped nuts or seeds for a heartier texture. Or try 1 cup whole wheat flour and ¾ cup all-purpose flour for a fluffier consistency.

Four images showing steps to make recipe including chopped apples with a knife. A bowl of chopped apples mixed in honey with a spatula. Muffin batter with chopped apples in a bowl with a wood spoon. A muffin pan with paper liners and batter in each cup.

How To Make Whole Wheat Apple Muffins

A quick overview of how to make these delicious apple muffins with full instructions in the recipe card below.

  1. Stir chopped apples with honey in a small bowl. Set this aside.
  2. Add whole wheat flour, cinnamon, baking powder, baking soda and salt together in a large mixing bowl.
  3. Add milk, egg and oil together in a separate bowl. Make a well in the center of dry ingredients and add the wet ingredients. Mix everything together. Fold the apple chunks into the batter.
  4. Add paper liners to the muffin tin and fill with ¾ of batter. Bake muffins until tops are golden and a toothpick comes out clean.

Leftover muffins can be stored in an airtight container at room temperature or chilled in the fridge up to 3-4 days. These muffins also freeze well. Add them to a freezer bag and store up to 3 months for maximum freshness. Frozen muffin can be thawed in the microwave for 30 seconds to warm and served with a little butter.

A dozen baked whole wheat apple muffins in a muffin pan.

Recipe Tips

  • Don’t forget to measure 2 cups of chopped apple into the batter. Do not add two full apples to the batter unless that measures 2 cups. Otherwise, there will be too many apples.
  • Chop the apples into small bite-size pieces. If they’re too big, the muffins won’t cook correctly.
  • Check the muffins for around 19 or 20 minutes to see if the tops are starting to turn golden brown.
  • If muffins are sticking to the paper cupcake liners, lightly spray the insides with nonstick cooking spray before adding the muffin batter.
  • Don’t overfill the muffin cups. Fill them ¾ full so there is room for them to rise.
Close up of six apple muffins lined side-by-side.

More Muffin Recipes

Whole Wheat Apple Muffins

Wholesome muffins made with fresh apples.
4.56 from 9 votes
Save Recipe! Pin This Print It
Prep Time: 10 minutes
Cook Time: 25 minutes
Total Time: 35 minutes
Servings: 12 muffins



  • Preheat the oven to 375°F.
    Wash and chop the apples into small bite-size pieces.
    Chopped apple with a knife on a cutting board.
  • Measure out 2 cups of chopped apples into a bowl with honey. Mix together and set aside.
    Two images of chopped apples in a white bowl with a spatula.
  • In a large bowl, mix together the flour, cinnamon, baking powder, baking soda and salt.
    Two images of a white bowl. First with flour, cinnamon and baking powder. Second is dry ingredients all mixed together with a spatula.
  • In a medium bowl, mix the milk, egg and oil.
    Two images of a white bowl with liquid ingredients inside.
  • Make a well in the center of the large bowl with flour mixture. Pour the wet ingredients in the center. Mix togethe until it forms a batter (do not overmix).
    Two images of a white bowl. First is dry ingredients with wet poured into the center. Second image is muffin batter and a wood spatula in bowl.
  • Add the chopped apples to the batter and gently fold them in until evenly combined.
    Two images of a white bowl. First has chopped apples dumped on top of batter with a spatula. Second is batter and chopped apples mixed together and a wood spatula.
  • Spoon the batter ¾ full into a muffin pan lined with paper muffin liners.
    An empty white bowl with a cookie scoop and leftover batter beside a muffin pan with uncooked muffins inside.
  • Bake for 20-22 minutes, or until a toothpick comes out clean when poked through the center of one muffin.
    Let cool 5 minutes, then transfer to a wire rack to cool completely.
    Two images of a muffin pan. First is raw muffin batter in the pan. Second is baked muffins in pan.


Calories: 131kcal | Carbohydrates: 28g | Protein: 4g | Fat: 1g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 1g | Cholesterol: 16mg | Sodium: 143mg | Potassium: 130mg | Fiber: 2g | Sugar: 15g | Vitamin A: 66IU | Vitamin C: 1mg | Calcium: 56mg | Iron: 1mg

The nutritional information provided is an estimate and is per serving.

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Recipe Rating


Sunday 28th of January 2024

I made but the batter was too liquid, is it supposed to be like that? I used white whole wheat pastry flour and 1/2 c maple syrup, although I wanted to have used brown sugar


Monday 29th of January 2024

A day after muffins were even better, nice moisture. Next time I will try with brown sugar.

Thank you for the recipe!


Monday 29th of January 2024

Hmm. It should be a normal batter consistency. You can always add a bit more flour to reach desired consistency though.

donna martin

Friday 6th of October 2023

I love this recipe! I had to make a brunch item for my husband's work potluck, and I was out of white flour, I didn't have a lot of milk and very little when I found this I was really excited. I got up early to make them and they came out fantastic! I did add my own little twist however, I chopped up some dried cranberry and mixed it in with the chopped apple, and then I made a crumble for the top and sprinkled it on. When I served it, I put some room temp real butter in a dish, added some cinnamon and honey and pushed it to one side then on the other took whipped cream cheese and also mixed honey and cinnamon to it and placed it next to the creamy butter mixture.

I can't wait for them to have it!

Grandma Elle

Sunday 5th of March 2023

These were somewhat dry, baked only 18 minutes at 375 degrees. The apples weren't soft. Perhaps should have used a softer baking apple. The flavor was ok but could have been more cinnamon or maybe nutmeg.


Sunday 26th of February 2023

Wonderful! Made these for tomorrow morning’s breakfast. Can’t wait!


Sunday 5th of February 2023

These muffins are delicious and my family loves them! I did add a little more cinnamon for flavor but other than that, they r a hit in our house!