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 really want to make these, but I can’t eat whole wheat flour (like many people these days I have trouble digesting it). I can tolerate white flour better. Any suggestions?
Maybe gluten free flour will work. Also maybe try my almond flour muffins? https://ifoodreal.com/almond-flour-banana-muffins/ Or lemon zucchini bread with almond flour? https://ifoodreal.com/healthy-lemon-zucchini-bread/
All purpose GF Flour worked for me! Try to find an 1 to 1 GF flour for best results as it will have the leavening additive included. Regular GF flour wont rise as well but still tasty. (I used King Arthur brand)
I made these for my Boot camp friends and they were gobbled up! And so appreciate the clean ingredients!
Fyi….I didn’t have enough applesauce and we had some leftover apple butter so I used that. I think they’re a bit more dense than normally, but still delicious. Had 3 whole muffins myself!
Awesome. Not sure what apple butter is but sounds like it worked for you. Thanks for sharing.
Delicious! The whole family enjoyed them. I used regular pancake syrup because it’s all I had on hand, but looking forward to picking up some honey and making the recipe again
This is exactly what I was looking for: a delicious muffin, healthy enough for breakfast and regular snacking, and uses up a bunch of carrot.
It works well doubled, and I cut the maple syrup in half and it was still sweet enough for me.
Thanks for this awesome recipe.
I love these, my kids love these. Happy to have found a non sugar sweet muffin. Easy to make.
I am following WW at the moment and these muffins come out to 4 points with all ingredients.
3 points omitting the raisins and nuts.
Super happy to hear that, Amanda!
Can’t these find be made in mini size tin? If so how long in the oven?
Yes you can. I would check after 15 minutes.
I am rarely able to follow a recipe without adding my own twist. For this I used my own blend of large-flake oats, oat and wheat bran and flax seed, substituting unbleached flour and ground almonds, proportionately, and mashed banana for the applesauce. I also added two tablespoons of grapeseed oil. I cooked the muffins in a 375 degree oven for twenty minutes. The result was extremely good, and I will be using your recipe as a blueprint again for sure. Thank you for sharing, Olena!
Can I substitute almond flour for whole wheat at a 1:1 ratio! I know gluten will help them rise but I just made your banana bread with calls for almond flour and the muffins came out great. Just wondering if any adjustments in liquids will need to be made by subbing.
I personally don’t think you I can substitute. Doesn’t work for me for reasons you listed. So I wouldn’t know.:)
Can I use sweetened cinnamon applesauce and leave out the honey/maple syrup?
I wouldn’t. It will offset the ratio of dry to wet ingredients. However, might be not the end of the world if you are OK with less sweet and not as properly tall/fluffy muffins for the sake of experiment.:)
Soooo good. This is the first “healthy” cake recipie that I’ve actually enjoyed. Moist and sweet. Will definitely be making these again.