Healthy Carrot Muffins made with applesauce, oats, whole wheat flour and maple syrup. Fluffy, light and moist carrot cake muffins!

I have updated these healthy carrot muffins to improve upon texture and lack of sweetness reported by some readers. Now you are getting foolproof carrot cake muffins!
And also developed cottage cheese carrot cake muffins recipe for those who are looking to add more protein to their diet.
They also freeze and defrost well, plus kids love them with a glass of cold milk for a healthy breakfast or an afternoon snack!
Why You’ll Love This Recipe

- Naturally sweetened: This healthy carrot muffin recipe is sweetened only with carrots, maple syrup and raisins.
- Wholesome: Made with whole grains like oats and whole wheat flour, plus walnuts and raisins.
- One bowl recipe: No need for 2 bowls to mix dry and wet ingredients separately.
- Perfect to make with kids: It’s one of the easiest muffin recipes to involve even the toddlers.
- Simple ingredients: While the list might seem long, they are all truly simple ingredients.
Reader’s Review
The muffins were delicious. I was so happy with the outcome that I made another batch right away so I can freeze some for later. This is my new favorite muffin recipe. Thank you for posting it. Greatly appreciated!
Angela
Ingredients for Healthy Carrot Muffins

- Carrots: You will need approximately 2-3 large carrots or 5-6 small/medium sized carrots. Use the small side of your grater or a vegetable peeler to grate carrots.
- Applesauce: Adds moisture instead of using only oil. I prefer to use unsweetened applesauce to keep them lower in sugar.
- Mild tasting oil: To add a bit of moisture. I used avocado oil but light olive oil, melted butter or coconut oil will work.
- Honey or maple syrup: I like the taste of maple syrup. You can use any other liquid sweetener like agave, honey etc.
- Eggs: Add lift and binding. I think chia eggs and flax eggs will work but muffins will rise less.
- Baking essentials and spices: Vanilla extract, cinnamon, nutmeg, baking soda, baking powder and salt.
- Whole wheat flour: I much prefer using whole wheat flour or spelt flour in baking for extra nutrients and fiber. You can also use white whole wheat flour or whole wheat pastry flour.
- Oats or oat bran: Recipe as pictured is made with oats. Note that carrot muffins with oat bran will just rise less.
- Add-ins: I love to use raisins and chopped walnuts for a carrot cake muffins taste, but feel free to use your favorite dried fruits or nuts.
Substitutions
- All-purpose flour: Use 1 3/4 cups of white flour instead.
- Gluten-free flour: Baking is a science and all-purpose gluten free flour is more moisture absorbent than wheat flour. You may get away with it but I haven’t tried. Also if you are experienced baker, you can add a bit more applesauce or oil.
- Oat flour: You can use oat flour but by its weight. If 1 cup of wheat flour weighs 120 grams, you will need same weight of oat flour.
- Almond flour or coconut flour do not bake the same, so I do not recommend this substitution.
- Oats: I have not tried steel cut oats. You may try quick cooking steel cut oats but muffins will rise less and will have more hearty chewy texture.
How to Make Healthy Carrot Muffins
Here is a step by step overview with photos. There is full recipe card below. All you need is just one bowl and a box grater!

- Combine liquid ingredients: Whisk the eggs, applesauce, maple syrup, oil and vanilla extract.
- Add leavening agents and spices: Now add cinnamon, nutmeg, baking powder, baking soda and salt.
- Mix: Whisk very well until you no longer see small white lumps.
- Add shredded carrots: Stir in grated carrots and please don’t squeeze them. The juice will ensure your muffins are moist.

- Add dry ingredients: Add oats and whole wheat flour to the carrot mixture, then gently mix with spatula until combined but not overmixed.
- Fold in raisins and nuts: And give a few stirs.
- Bake the muffins: Place batter evenly into a 12 muffin tin and bake the muffins for 24-25 minutes in 350 F preheated oven. The muffins are done when a toothpick inserted in the middle comes out clean.
- Cool: Rest in muffin cups for 5 minutes, then transfer to cool on a wire rack to cool a bit more.
Tips for Best Results
Here are my top tips for the best healthy carrot muffins after perfecting this recipe for over 8 years.
- You can use yogurt instead of applesauce: Plain yogurt or protein-rich Greek yogurt will work. Just keep in mind your muffins will be less sweet, so add extra 2-3 tablespoons of maple syrup.
- Do not over bake: Remove muffins from the oven as soon as toothpick comes out clean to avoid dry muffins, even if they look not too browned. Muffins keep cooking with residual heat.
- Let muffin batter sit: If you like very soft oats in muffins, let batter sit for 10 minutes before dividing it into a muffin pan.
- Don’t squeeze shredded carrots: That’s where carrot muffins get their moisture from.
- Mini or jumbo muffins: You can bake mini carrot muffins for about 11 minutes. For jumbo carrot muffins, bake them for 30 minutes or so. Always do a toothpick test.

Variations
- Tropical: Add 1/2 cup of chopped pineapple pieces that have been gently squeezed, if from a can; and 1/4 cup coconut flakes.
- Different warming spices: Use ground cloves, ginger or allspice vs. cinnamon or nutmeg.
- Sweeter muffins: Sprinkle with coarse sugar or brown sugar before baking.
- Topping: After muffins have cooled, use a drizzle from healthy coffee cake to turn them into carrot cake muffins!
- Frosting: Transform your muffins into a dessert with Greek yogurt frosting, healthy cream cheese frosting or healthy buttercream.
How to Store
I usually keep muffins on a counter for a few days. At that point, if any are left (happened only once here), I pop them into an airtight container in the fridge to prevent dry and stale muffins.
You can also freeze them for up to 3 months in the freezer. Then just thaw overnight in refrigerator or on a counter for 3-4 hours.
Storage Tip
Don’t miss my detailed posts how to store muffins and how to freeze muffins to keep your leftover muffins fresh longer.
More Healthy Muffins Recipes
- Banana carrot muffins
- Zucchini carrot muffins
- Healthy morning glory muffins
- Healthy zucchini muffins
More Carrot Recipes to Try


Healthy Carrot Muffins
Equipment
Video
Ingredients
- 2 large eggs
- 3/4 cup applesauce, unsweetened
- 1/4 cup oil, I use avocado oil
- 1/2 cup + 2 tablespoons maple syrup or honey
- 1 teaspoon pure vanilla extract
- 1 1/2 teaspoons cinnamon
- 1/2 teaspoon nutmeg
- 2 teaspoons baking powder
- 1/2 teaspoon baking soda
- 1/2 teaspoon salt
- 1 1/2 cups grated carrots, packed
- 1 cup rolled oats, quick oats or oat bran
- 1 1/3 cups whole wheat flour
- 1/2 cup raisins
- 1/2 cup walnuts, coarsely chopped
- Cooking spray, I use Misto
Instructions
- Preheat oven to 350 degrees F, line 12 muffin tin with muffin liners and spray with cooking spray. Set aside.
- In a large mixing bowl, add eggs, applesauce, oil, maple syrup, vanilla extract and whisk. Add cinnamon, nutmeg, baking powder, baking soda, salt and whisk very well until no lumps are visible.
- Add grated carrots and stir with spatula to mix. Add oats and whole wheat flour, then gently mix until combined. Do not over mix. Stir in raisins and nuts.
- Distribute batter evenly between 12 openings of a tin (I used a regular ice cream scoop) and bake for 24-25 minutes or until a toothpick inserted in the centre comes out clean.
- Remove carrot muffins from the oven, let cool for 5 minutes and transfer to a cooling rack to cool off more.
Notes
- Store: In an airtight container for 2-3 days. Refrigerate after for a few more days.
- Freeze: In an airtight container for up to 3 months. Thaw muffins overnight in refrigerator or on counter for 3-4 hours.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.














I loved the sound of this recipe and I immediately wanted to make it for breakfast, but I hope you dont mind I made a few changes due to what I had available.
1) l used AP Flour (1 cup plus another 2-3 tbsps)
2) I threw in some grated ginger and oranges because why not LOL
3) I used about 1/4 cup of honey because I considered the sweetness and added liquid from the orange.
4) I used regular apple sauce, not unsweetened because that’s all I had
5) I threw in an omega-3 mix that had pumpkin seeds, almonds, dried cranberries, and golden raisins.
It was amazing and I thank you so much for this recipe <3
Thanks for your comment and glad it worked out with the ingredients you had on hand Melinda!
Did you make any changes to the recipe? Didn’t puff up like mine in the pics? I think maybe old baking powder. It does expire. Rolled oats are not the fault. Seems like lack of chemical reaction.
I accidentally read the recipe wrong and only beat the eggs together with all the wet ingredients ya. Thank God they still turned out well consistency-wise. Also since we don’t have applesauce I substituted it for yogurt. It makes it not very sweet which is great but then the kids may not really like them
Excellent!! I love my traditional carrot cake with crushed pineapple, so I added that to the recipe as well. I also soaked the raisins in the pineapple juice for 30 minutes to make them more delicious. My husband and I loved this-a healthy keeper! This was the first recipe I have tried from your site. I will look for more! Thank you!
Hi Charlise! Don’t be shy to leave me a comment when you try any of my other recipes!
Great recipe, just in time, I have a lot of carrots to use up
Your carrot muffins are delicious yummy
Thank you
Since you’re from Ukraine do you know how to make borscht sour
Maybe they call it kava
Fermented beets
I have borscht recipe. Not sure what kava is or we never made fermented beets. There are a few regions with very different cooking. 🙂
OMG this is a WINNER!! I made mini muffins and baked for 20 minutes – Perfect! And I used Almond.
Tammy! Yay! So happy to hear that you liked this muffin recipe!
I had a container of cream cheese frosting in my fridge that’ll expire this month so I wanted some carrot muffins to use it up. But I’m trying to eat somewhat healthy so I googled healthy carrot muffins. I decided to try this recipe. However I didn’t add the raisins and nuts because I prefer carrot cake/muffins without it. I halved the recipe in case I didn’t like them. But I was pleasantly surprised. They are good. But I have to be honest, I did put quite a bit of frosting on the one I tried!
I needed a quick recipe to bring to coffee with friends before we went on a long walk. I was able to quickly pull the recipe together and get them baked in time. They came out perfect! My friends loved the healthy AND flavorful treat, and both requested the recipe. A keeper! Thank you!
I’m so happy you and your friends loved the recipe, Sandy. Thanks for sharing that with me!
What is the measurement if I want to make the muffins with just oat flour and no whole wheat flour.
Has to be whole wheat.
I actually did make these carrot muffins with only oat flour. I used 2.5 cups of oat flour. I do not know how they will turn out since they are still baking, but I hope it turns out good.
How did it work with just oats? I would like to try it this way as well.
A great go-to breakfast and snack. My baby loves them, too!
So happy to hear, Melinda!