Healthy Apple Muffins

It is so easy to make these healthy apple muffins (gluten-free) made with fresh apples, cinnamon, carrots, flax meal, and sweetened naturally with maple syrup! It takes two steps by blending together fresh apples and carrots with the wet ingredients then mixing those with the dry ingredients.

Apple muffins

Time to make healthy apple muffins that everyone loves! We’ve got loads of healthy muffin recipes here like our chocolate chip spinach muffins, banana nut muffins, healthy chocolate chip muffins, healthy carrot muffins, zucchini pumpkin muffins, gluten-free blueberry oat muffins! Each muffin, like these healthy apple muffins, are filled with fresh fruits or vegetables, fiber, and uses only natural sugars and gluten-free flour.

Why this recipe is the best

These amazing apple muffins are awesome to make in the evening to save time on busy mornings. Enjoy them for breakfast and a nourishing snack in the day. They taste like a twist between an apple pie filling with apple cinnamon flavors and have no applesauce, just loads of fresh apples blended in!

They are incredibly healthy, made gluten-free, dairy-free, with wholesome fruits and vegetables, and natural sugar. These easy apple muffins are treats you feel good about eating and keep you full and fueled for hours thanks to loads of fiber!

Try them with a sprinkle of coconut sugar (natural sugar), demerara sugar, or turbinado sugar (raw can sugar and less processed) on top!

Healthy Apple Muffin Recipe Tips

  • Use honeycrisp apples for a sweeter baked good or granny smith apples work well for baking.
  • We blend everything in a blender so there are no chunks – just applesauce flavor. You can reserve some of the fresh apple and chop or grate them into the muffin batter to add more texture.
  • You can substitute maple syrup for agave syrup or honey. If using honey the apple muffins will brown quicker so check for doneness after 18 minutes by inserting a toothpick in the center which should come out clean.


  • 2 honeycrisp apples or granny smith apples (2 cups cubed)
  • 1 carrot (1 cup chopped)
  • maple syrup
  • avocado oil
  • unsweetened almond milk
  • 2 eggs
  • vanilla extract
  • gluten-free flour
  • flax meal
  • cinnamon
  • nutmeg
  • ginger powder
  • baking powder
  • baking soda
  • salt

How to make healthy apple muffins

Preheat the oven to 350 degrees F. Line a muffin tin with paper liners or spray a silicone muffin pan.

In a blender, add the apple, carrot, eggs, oil, maple syrup, almond milk, and vanilla extract. Blend a few seconds until it is combined. combine gluten-free flour, tapioca flour, baking soda, salt, cinnamon, nutmeg and ginger mix to combine and set aside.

In a large bowl combine the gluten-free flour, flax meal, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt. Mix to combine then pour in the wet ingredients into the dry ingredients and mix the batter to combine.
Scoop the batter equally into the muffin pan cups.

Bake for 20-22 minutes or until tops are slightly brown and a toothpick inserted comes out clean. Let the apple cinnamon muffins cool slightly before removing and transfer to a cooling rack to finish cooling.

How to store muffins

Store these healthy apple muffins in a sealed airtight container on the counter for 3 days or in the refrigerator for 5 days. To freeze the muffins, place them in a freezer zip bag and make sure all the air is removed before closing the bag. Freeze for up to 3 months.

Measuring Gluten-Free Flour

Flour tends to compact during packaging and shipping. To measure the flour, fluff it in the bag then scoop it with a spoon into a measuring cup. Use the back of a knife to level off the flour. 

Frequently Asked Questions

What is the healthiest muffin to eat?

We have loads of healthy muffins you will love! Healthy muffins contain no processed sugars, and include fiber and wholesome ingredients. Try these basic recipes:
Oatmeal Chia Seed Muffins
Gluten-Free Pumpkin Muffins
Healthy Chocolate Chip Muffins
Chocolate Chip Spinach Muffins
Healthy Carrot and Avocado Muffins
Oil-Free Zucchini Pumpkin Muffins
Banana Nut Muffins
Blueberry Lemon Yogurt Muffins
Oatmeal Muffins
Gluten-Free Blueberry Muffins
Banana Zucchini Muffins
Grain-Free Pumpkin Muffins

Can muffins be healthy?

Yes, muffins can be healthy! Choose muffins that are not made with processed ingredients or in packaging. Make them with wholesome ingredients that include fresh fruits, vegetables, oats, fiber, grains, and nuts.

What is the best apple to use in muffins?

Honeycrisp apples or Granny Smith apples are the best apples to use in these muffins. We always have honeycrisps around, which create a sweeter muffin, and granny smith muffins add beautiful flavor and texture as well when baked.

If you make our healthy apple muffins from Delightful Mom Food I would love to see your creations and share it! Follow along with me on INSTAGRAM, PINTEREST, FACEBOOK, YOUTUBE and TWITTER to be featured and for more recipe inspiration! And don’t forget to rate the recipe in the recipe area and leave a comment below.

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