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These Healthy Apple Muffins are moist, fluffy and perfectly apple-y. Lightly sweetened with maple syrup, apple sauce and apples, these healthy muffins are free of refined sugar, made with wholesome whole wheat and easily made dairy free.

Two healthy apple muffins stacked, one with a bite taken out of it.

Just call me the muffin lady. Not sure when I decided that my calling was making healthy muffins that are also moist, light, fluffy and delicious. Actually I do know – it was when I first developed my Peanut Butter Banana Muffins for my toddler. Well, here I am again, this time with THE BEST healthy apple muffins. These muffins are packed with apple flavor, plus maple, cinnamon and spices.

Ingredients for healthy apple muffins - apples, applesauce, apple cider vinegar, eggs, butter, vanilla, spices, baking powder, baking soda, maple syrup, milk.

What makes these apple muffins healthy?

Everyone has a different idea of what healthy means, but since I developed this recipe for my kids, my main focus was making them low in sugar and high in nutrients like fiber and protein. I also wanted to make these easily dairy free since my baby has a milk allergy. But they can also be made with dairy for those who wish to do so.

What are the ingredients for Healthy Apple Muffins?

  • Grated Apple – adds sweetness, moisture, and lots of apple flavor!
  • Unsweetened Apple Sauce – adds more apple flavor, moisture and natural sweetness.
  • Pure Maple Syrup – adds a touch of sweetness without using refined sugar.
  • Butter – adds flavor and moisture. You can use vegan butter for dairy free
  • Eggs – for moisture and binding
  • Milk – you can use dairy milk or non dairy milk
  • Apple Cider Vinegar – the secret ingredient! This is what makes them so tender and fluffy. It does NOT make them taste like vinegar at all.
  • Pure Vanilla Extract – more flavor!
  • Whole Wheat Pastry Flour – using whole wheat pastry flour is what makes these super light and fluffy with the nutritional benefits of whole wheat flour.
  • Spices – cinnamon, ginger, nutmeg, and clove. These spices together with apples are a match made in heaven!
  • Baking Soda – makes the muffins rise.
  • Baking Powder – This is different than baking SODA and yes, you need both of them.
  • Salt – don’t skip it! Without salt, these muffins will be bland.
Two bowls, on with wet ingredients and one with dry ingredients, before mixing together.

How many calories are in a homemade healthy apple muffin?

My main focus when creating healthy muffin recipes for kids is not how many calories they have, but that they are packed with nutrition that kids (and adults) need – protein, calcium, and fiber for example. I also like to keep most foods low in sugar if possible. The nutrition information for these healthy apple muffins can be found below the recipe. One healthy apple muffins contains approximately 170 calories, 5 grams of fat, 28 grams carbohydrates, 3 grams of fiber, 4 grams pf protein. Keep in mind these are estimates and will vary based on the ingredients you use.

How to make muffins that are light and fluffy instead of dense and tough

It’s important to mix the wet and dry ingredients in two different bowls. Mix them very well. After combining the wet ingredients with they dry ingredients, you want to just mix them until they come together. Do this by hand and don’t use a mixer. If you over mix the batter, the muffins will be tough.

Another trick I used for making these apple muffins fluffy was using vinegar in the recipe. Yes, you read that correctly – vinegar! Why does vinegar make muffins fluffy? It increases the acidity of the batter and reacts with the baking soda to create a better rise. It is similar to using buttermilk or yogurt in a recipe, like in my blueberry buttermilk pancakes.

You may be nervous adding vinegar to a muffin recipe, but don’t be. This doesn’t make them taste like vinegar at all. It just makes the muffin better.

Healthy apple muffins on a cooling rack

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Healthy Apple Muffins

Prep 10 minutes
Cook 25 minutes
Servings 12 muffins


Wet ingredients

  • ¼ cup unsalted butter melted. Can use vegan butter or dairy butter.
  • 3/4 cup unsweetened apple sauce
  • 1/2 cup pure maple syrup
  • 2 cups apple grated, with or without peel. (1-2 apples)
  • 2 eggs beaten
  • ¼ cup milk can use dairy milk or dairy free milk
  • 1 teaspoon apple cider vinegar
  • 1 teaspoon pure vanilla extract

Dry ingredients

  • 2 cups whole wheat pastry flour
  • 1 and 1/2 tsp cinnamon
  • ½ tsp ground ginger
  • ¼ tsp grated nutmeg
  • ¼ tsp ground clove
  • 1 tsp baking soda
  • 1 tsp baking powder
  • 1/4 teaspoon salt


  • Preheat oven to 425 degrees F. Prepare a muffin tin by spraying with non stick spray or using muffin liners.
  • In one bowl, mix together the wet ingredients – melted butter, apple sauce, grated apple, eggs, maple syrup, milk, apple cider vinegar, and vanilla until well combined.
  • In another bowl, whisk together the dry ingredients – flour, spices, salt, baking powder and baking soda until well combined.
  • Add the dry ingredients to the wet ingredients, mix until just combined. Do not overmix.
  • Evenly divide the batter between 12 muffin cups.
  • Bake the muffins at 425 degrees for 5 minutes. After five minutes, leave muffins in the oven but reduce heat on oven to 350 degrees. Bake for another 17-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Remove muffins from the oven to a cooling rack. As soon as muffins are cool enough to handle, remove them from the muffin tin and finish cooling on the cooling rack. Allow to cool completely before storing.
  • Muffins can be kept in a sealed container at room temperature for 1-2 days. Muffins can be frozen for up to 3 months.


To freeze: Allow to completely cool before freezing.  Individually wrap in plastic wrap and then store in a freezer bag.  Muffins can be thawed in the refrigerator overnight or quickly thawed and warmed up in the microwave for 30-45 seconds. 
To make dairy free: use vegan butter and non dairy milk such as unsweetened almond milk.


Serving: 1muffin | Calories: 170kcal | Carbohydrates: 28g | Protein: 4g | Fat: 5g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 1g | Cholesterol: 38mg | Sodium: 185mg | Potassium: 141mg | Fiber: 3g | Sugar: 12g | Vitamin A: 183IU | Vitamin C: 1mg | Calcium: 59mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Did you like this recipe?Please comment, rate and share! And don’t forget to tag me on Instagram @foxandbriar AND #foxandbriar so I can see what you made!

Disclosure: This post contains affiliate links, which means that if you purchase the items I recommend through the links I provide, I get a small commission at no extra cost to you. For more info, please see my disclosure policy. Thanks for supporting Fox and Briar!

Hello! I’m Meghan.

I am so glad that you are here! I am the recipe developer, photographer, and writer here at my blog Fox and Briar. I am a passionate, self-taught home cook and believe that most things are better homemade and that good food doesn’t need to be complicated.

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1 Comment

  1. This is the second muffin I have made of yours today !!! This is another winner ! I added cranberries and some flax seed and they came out moist and delicious. I am enjoying one with tea as I type this. 🙂