These healthy apple cinnamon muffins are great to prep for back-to-school mornings, freezer breakfast or snacks, or just a hearty fall muffin! They use Greek yogurt, honey and apples in them to make these a healthier treat!

I made these muffins to freeze for back-to-school breakfasts– they will be a great addition to my freezer breakfast egg muffins and breakfast burritos!
We have 3 apple trees on our farm, and these are a great way to use up the apples so that none go to waste– I also like to make them into slow cooker applesauce or apple bars.
Why you will like this recipe
- uses healthier ingredients (Greek yogurt, honey, apples) which makes these a great breakfast option
- freezes well for meal prep
- these are a very moist muffin!
Ingredients in Healthy Apple Cinnamon Muffins
- All Purpose Flour– you can try this with other “healthier” types of flour blends, but this is the only kind I have tried in this recipe.
- Apples– you need approximately 2 medium to large apples. One to dice up, and one to grate.
- Applesauce – unsweetened. If you use sweetened applesauce, it will be OK, but you may just have a little more added sugar in your recipe. I used our homemade applesauce. I have also used pear sauce–and couldn’t tell the difference! Here is a recipe to make your own slow cooker applesauce.
- Eggs – 2 large
- Vanilla Extract
- Plain Greek Yogurt– any kind, and any “fat” percentage
- Honey – I use local raw honey
- Sugar – white, granulated sugar
- Cooking oil– olive, coconut, vegetable oil all work fine.
- Baking soda and baking powder
- Salt
- Cinnamon – for the perfect fall baking combo!

Substitutions and Variations
- Flour: I used all-purpose, but feel free to substitute with a gluten free blend or whole wheat, etc.
- Sweetener: I personally still like to use a little bit of white sugar in my recipes. You can substitute the white sugar for additional honey or maple syrup.
- Applesauce: I have subbed applesauce with pear sauce, and you couldn’t tell the difference!
- Spices: feel free to add 1/4- 1/2 tsp of cloves or nutmeg for a even more “fall” recipe.
How to make Apple Muffins
- Mix your dry ingredients
First, you will mix all the dry ingredients together (flour, salt, baking soda, baking powder, cinnamon)
- Prep your apples
As mentioned above, you need 1 apple diced small and 1 apple grated. Use a cheese grater to grate your apple (I left the peel on). Then just dice up the other one- leave the peel on if you wish.
- Add apples to dry mix
Fold your apples into the dry mixture.
- Wet Ingredients
Combine all wet ingredients (oil, sugar, honey, eggs, applesauce, yogurt, vanilla)
- Put it all together!
Now, pour your wet ingredients into your “dry mix” and use a large rubber spatula or spoon to mix all together. Bake at 425 F for about 15 minutes until toothpick comes out clean.
- What kind of muffin pan do you use?
I highly recommend a silicone muffin pan– they are low cost and make both removing the muffins from the pan, and washing the pan–soo easy!

Muffin FAQ
I usually use apples from my farm, and they are just “wild” so they don’t have a “type”. I think any kind of apples used for baking will work just fine! (honeycrisp, cortland, jonagold, etc)
This is totally up to you. I peeled the skins on the apple that I diced-BUT only because I have young kids and I was worried they would see the peel on the muffin (they can be picky). I left the peel on the apple that I grated since it was smaller.
When the toothpick comes out clean.
They can definitely be frozen.
Freezer Instructions: let cool completely. Transfer to sheet pan and flash freeze for 1 hour. Then, transfer to a gallon freezer bag. Label and store in freezer for up to 3 months. Set on counter to thaw.
Plain Greek style yogurt, but you can use any fat content you’d like.
Do not overmix the batter and avoid overbaking. The applesauce and yogurt already help these become a very moist muffin!
No, there is flour in them. Try substituting regular flour 1:1 with a gluten free flour.

What to pair with these muffins
- breakfast sausage or a yogurt parfait for breakfast
- slather peanut butter on the muffin (or other nut butter)
- pair with a smoothie–or eat just on its’ own!
More recipes you might enjoy
- high protein bagels if you’re looking for another healthier carb option
- Zucchini Chocolate Chip Mini Muffins
- Pumpkin Chocolate Chip Muffins
- crockpot applesauce – great way to use up apples
- protein pancakes with oats – protein for breakfast–always a win!
- cinnamon apple bars – a great apple fall dessert
- more muffin tin recipes: egg muffins and lasagna cups— both very freezer friendly too!
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I hope you love these simple, healthier muffins! – Bobbi Jo


Healthy Apple Cinnamon Muffins – SIMPLE!
Equipment
- 1 muffin pan I love using silicone pans
- 2 mixing bowls medium size
- common measuring utensils
Ingredients
- 1-3/4 cup all purpose flour
- 1-1/2 tsp baking powder
- 1/2 tsp baking soda
- 1 tsp ground cinnamon
- 1/2 tsp salt
- 1 cup grated apple (about 1 large apple)
- 1 cup diced apple (1 medium appx)
- 1/3 cup cooking oil I used olive oil, but coconut oil or vegetabe oil would work
- 1/2 cup plain greek yogurt
- 1/2 cup unsweetened applesauce if using sweetened, it will just be a sweeter muffin
- 2 large eggs
- 2 tsp vanilla
- 1/4 cup granulated sugar
- 1/4 cup honey or maple syrup
Instructions
- Preheat oven to 425 F.
- In a medium to large bowl, combine your dry ingredients with a whisk (flour, baking soda, baking powder, cinnamon, salt).
- Prepare apples: next, dice 1 cup of apple into small pieces. You can remove peel or keep it on. Then, use a cheese grater to grate 1 cup of apple. (I kept peel on). Add the apples to your dry ingredients and gently stir. Set aside.
- Now, combine your wet ingredients. (Oil, honey, sugar, eggs, yogurt, applesauce, vanilla).
- Pour the wet ingredients into the dry ingredients and mix together. I used a big rubber spatula. Mix until combined. Then, scoop into a muffin pan- about 1/4 cup of batter in each section. This will make 12 muffins.
- Bake for approximately 15 minutes, or until toothpick comes out clean and tops are golden. Let cool and enjoy!
Notes
Nutrition
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Great taste and very moist.
Glad to hear you liked them!!
So moist, freezer friendly and a family favorite!