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Home Recipes By Meal Breakfast

Healthy Apple Cinnamon Muffins

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By: Erin Antoniak • Updated On June 20, 2026
Jump to Recipe

This is a recipe for Healthy Apple Cinnamon Muffins which make the perfect, simple breakfast for fall. They are made with wholesome ingredients like maple syrup, whole wheat flour, and coconut oil.

tray of apple cinnamon muffins

Delicious and easy healthy apple cinnamon muffins

Muffins are one of my favorites, though they’re a breakfast food that often gets a bad rep! Many deem them as unhealthy as donuts, despite the fact that they don’t come with icing or sprinkles (I suppose in that case they’d be cupcakes!). However, muffins don’t have to be unhealthy. In fact, you can easily sneak nutrient-rich ingredients into any batter.

This easy healthy apple cinnamon muffin recipe is a lighter, more nutritious version of classic variations. They’re filling and taste extra delicious when enjoyed warm and fresh out of the oven! Add a slab of nut butter, crumble them into your favorite yogurt, or enjoy as-is.

These healthy apple cinnamon muffins make for an easy on-the-go breakfast but could also work as a healthy choice for an afternoon or night snack.

bite out of apple cinnamon muffin

Ingredients in this apple cinnamon muffin recipe

Personally, I think many of the grain-free or gluten-free muffins recipes that I’ve made can feel really heavy and dense. They also seem to really get almost “wet” if you don’t eat them within the first day. I don’t know why this happens but it’s weird and it is not how I want to enjoy my muffins.

Here’s everything you’ll need to get started:

  • Flour: The base of the muffin batter begins with 1 3/4 cups gluten-free flour or white whole wheat flour.
  • Cinnamon: Start creating that delicious apple cinnamon flavor by using 1 tbsp of cinnamon.
  • Nutmeg: Add a slightly nutty taste with 1/4 tsp of nutmeg.
  • Ginger: Follow the nutmeg with 1/4 tsp of ground ginger.
  • Baking soda: Then, help the muffins bake properly by including 1/2 tsp of baking soda.
  • Salt: Be sure to add 1/2 tsp of salt — it makes all of the difference!
  • Eggs: 2 room temperature eggs will help bind the dry ingredients together.
  • Maple syrup: Sweeten things up by including 1/2 cup of maple syrup. If preferred, you can use honey!
  • Vanilla: Don’t forget the vanilla! Use 1 tsp.
  • Coconut oil: Contribute to the texture of the muffins by including 1/2 cup of melted coconut oil.
  • Applesauce: Last but not least, finish off the batter with 1/2 cup of unsweetened applesauce.
 

Kitchen tools required to make healthy apple muffins

When it comes to kitchen tools, you will need various mixing bowls as well as a muffin tin and liner. Below is a full list of everything you can expect to use:

  • Muffin tin
  • Muffin liners or nonstick spray
  • Large mixing bowl
  • Stirring utensil
  • Small mixing bowl
  • Whisk
  • Baking spatula
  • Measuring cups: 1/4 tsp, 1/2 tsp, 1/2 cup, 3/4 cup, and 1 cup
apple cinnamon muffin with chocolate spread

How to make healthy apple cinnamon muffins

This muffin recipe comes together in no time. We’ll prepare it similarly to other baked goods, starting with the wet ingredients, followed by the dry. Then, we’ll simply combine and bake!

To begin, preheat the oven to 350°F.

Combine all of the dry ingredients (flour, cinnamon, nutmeg, ginger, baking soda, and salt) in a large mixing bowl.

Then, whisk the eggs together in a separate small mixing bowl.

To the bowl with the eggs, add your sweetener of choice (maple syrup or honey), followed by the vanilla and coconut oil.

Pour the wet ingredients into the dry and stir to combine.

Gently fold in the applesauce, but do not overmix! Doing so will cause the muffins to have a puffy dome.

Once mixed, fill the prepared muffin tray with the batter. The muffin tray should have muffin liners or be sprayed with non-stick spray.

Bake for 18-20 minutes or until the muffins become golden and/or a toothpick comes out clean.

Substitution Tip

Substitution Tip

I recently picked up the gluten-free all-purpose flour from Trader Joe’s and after some recipe testing, I developed a recipe that yielded the lightest, most fluffy muffins (gluten-free or not) I’ve had in a while. I also tested these with whole wheat flour and they turned out delicious!

That being said, there are a handful of ingredient swaps just like that one that you can use in this recipe.

Flour
Feel free to use gluten-free all-purpose flour or whole wheat flour. Your preference!

Baking Soda
Did you know that baking soda can be substituted with baking powder? It’s true! For this recipe, you can use 1.5 tsp of baking powder if you find yourself low or out of baking soda.

Eggs
If you want to skip the eggs for a vegan muffin, simply up the amount applesauce. Add an extra 1/2 cup, amounting to 1 cup total.

Coconut oil
Don’t fret if you’re out of coconut oil. Though I prefer this in my baked goods, vegetable or canola oil will also work.

apple cinnamon muffin in tray

Storing leftovers

I love making large batches of muffins to freeze for later. It makes future breakfast so easy, especially when we have a particularly busy week!

If freezing muffins, simply add the baked and cooled muffins to a freezer bag or airtight container. Freeze for up to 2 months.

When ready to enjoy, just thaw, keep at room temperature, and grab-and-go.

If you liked this recipe, you’ll want to try these!

If you liked this recipe, you’ll want to try these!

Muffin recipes are some of my favorites to whip together. Apart from being easy to prepare, they make such convenient snacks! Here are some more delicious flavors that you can try!

  • Pumpkin Chocolate Chip Muffins
  • Blueberry Crumble Yogurt Muffins
  • Banana Chocolate Chip Oat Muffins
  • Healthy Chocolate Peanut Butter Banana Muffins
apple cinnamon muffin

tray of apple cinnamon muffins
Erin Antoniak

Healthy Apple Cinnamon Muffins

5 from 4 votes
This is a recipe for Healthy Apple Cinnamon Muffins which make the perfect, simple breakfast for fall. They are made with wholesome ingredients like maple syrup, whole wheat flour, and coconut oil.
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 20 minutes mins
Total Time 30 minutes mins
Servings: 10 -12 muffins
Course: Breakfast, dairy-free, gluten-free, grain-free, Snack
Cuisine: American
Calories: 227
Ingredients Method Nutrition

Ingredients
  

  • 1 3/4 cups gluten-free flour or white whole wheat flour
  • 1 tbsp. cinnamon
  • 1/4 tsp nutmeg
  • 1/4 tsp ground ginger
  • 1/2 tsp. baking soda
  • 1/2 tsp. salt
  • 2 eggs room temp
  • 1/2 cup maple syrup or honey
  • 1 tsp. vanilla
  • 1/2 cup coconut oil melted
  • 1/2 cup unsweetened applesauce

Method
 

  1. Preheat oven to 350F
  2. Combine dry ingredients in large bowl
  3. Whisk eggs together in small bowl
  4. Add sweetener of choice, vanilla and coconut oil to whisked eggs
  5. Combine wet ingredients into dry and stir to combine but
  6. Gently fold in applesauce, DO NOT OVERMIX. Overmixing will cause your muffins to grow a puffy dome.
  7. Fill prepared muffin tray (cups or sprayed with non-stick spray)
  8. Bake for 18-20 minutes or until golden and toothpick comes out clean

Nutrition

Calories: 227kcalCarbohydrates: 29gProtein: 3gFat: 12gSaturated Fat: 9gPolyunsaturated Fat: 0.5gMonounsaturated Fat: 1gTrans Fat: 0.003gCholesterol: 33mgSodium: 177mgPotassium: 65mgFiber: 3gSugar: 12gVitamin A: 55IUVitamin C: 0.2mgCalcium: 52mgIron: 1mg

Tried this recipe?

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5 from 4 votes

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Recipe Rating




  1. Murray says

    Posted on 2/7 at 9:01 pm

    5 stars
    So good!! I added a cinnamon streusel on top from one of your blueberry muffin recipes and OMG… yum.

    Reply
    • Erin says

      Posted on 2/8 at 4:59 pm

      Hi Murray, so glad you loved them and great idea! 🙂

      Reply
  2. Kellen says

    Posted on 1/5 at 8:03 pm

    5 stars
    Omg why have I never made these? So delicious I want to eat them all!

    Reply
    • Erin says

      Posted on 1/6 at 12:27 pm

      Hi Kellen, so happy you loved them!! 🙂

      Reply
  3. Clara says

    Posted on 9/20 at 9:50 am

    5 stars
    I made these muffins, with a few modifications, and they came out delicious and fluffy. I only had 3/4 cup gluten-free flour left in my pantry, so I added 1 cup almond flour. I didn’t want my muffins to be greasy, so, because I used almond flour, which’s high in fat, I halved the coconut oil and added 1/4 cup applesauce. The baking time had to be longer, about 32-35 minutes. Do you think I could reduce the honey to 1/3 cup? They were a bit too sweet.

    Reply
  4. Jessica says

    Posted on 9/18 at 9:47 am

    Can you use fresh apples?

    Reply
    • Erin says

      Posted on 9/18 at 6:05 pm

      Hi Jessica, yes that should be fine! It may take a little longer to cook so they are fully cooked through.

      Reply
  5. Lisa says

    Posted on 7/12 at 3:21 pm

    Hi there! This looks delicious! If I don’t have coconut oil on-hand, will an equal amount of butter suffice? Thank you! Can’t wait to try this recipe!

    Reply
    • Erin says

      Posted on 7/12 at 5:23 pm

      Hi Lisa, thanks and hmm I haven’t tried it with that sub but possibly. Feel free to give it a try or use another oil like vegetable. Let me know what you use and how they come out!

      Reply
  6. Alyssa A says

    Posted on 12/22 at 12:53 pm

    Delicious and so moist!

    Reply
    • Erin says

      Posted on 12/23 at 12:07 pm

      Hi Alyssa, thanks for your kind words!

      Reply
  7. Olivia M says

    Posted on 9/9 at 5:39 pm

    5 stars
    SO good with peanut butter!

    Reply
    • Erin says

      Posted on 9/9 at 7:34 pm

      So glad you like them!! Thanks for sharing 🙂

      Reply
  8. Summer says

    Posted on 2/16 at 4:15 pm

    I just made these in a 9×9 cake pan and added walnuts and a frosting made with Kite Hill yogurt, cream cheese, and a little powdered sugar. Soooo yum! I absolutely love your baking recipes.

    Reply
    • Erin says

      Posted on 2/17 at 9:06 am

      WOW! That sounds delicious!!! I’m so glad you are enjoying!! 🙂

      Reply
  9. Sederiya says

    Posted on 9/18 at 11:29 pm

    Your recipes give me life! I cant wait to try these. I was looking for a nice snack that wasn’t a loaf for next week. These will be perfect!

    Reply
    • Erin says

      Posted on 9/19 at 5:53 pm

      Aw, you are TOO nice!! Hope you enjoy them when you make em 🙂

      Reply
  10. Dee says

    Posted on 5/12 at 7:25 pm

    Excited to try these! Most of my gluten free baking turns out mushy, so I have high hopes that these will be a turn around for me.

    Reply
    • Erin says

      Posted on 5/14 at 5:56 pm

      You will LOVE these then! I was so incredibly happy with the texture. If you give them a try, let me know!

      Reply
  11. Allie @ Miss Allie's Kitchen says

    Posted on 5/10 at 10:07 am

    It’s SOOO hard to feel lost in the beginning. You’re cranking out content wondering if people are watching, but if they aren’t already, they will be. You seem to have SUCH a knack for healthier baked goods which is such a great niche. You’re doing all of the right things and these muffins look BOMBBBBB!

    Reply
    • Erin says

      Posted on 5/10 at 12:38 pm

      Yes girl, you get it. I think its key to persevere and keep it up. I’m so excited about my future and I’m so glad we connected!

      Reply

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I’m Erin. Creator of Erin Lives Whole, a food blog with delicious and easy healthy recipes that will leave you feeling good. We’ve got everything from wholesome baked goods to comforting savory dishes. I can’t wait to see what you whip up! Read More...

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