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A whole-wheat muffin you’ll actually enjoy! These Healthy Carrot Muffins are tender, sweetened with honey, and made with heart-healthy olive oil and protein-rich Greek yogurt. A dash of warm spices and a sweet-crunchy topping make these an absolute winner.
I’m a food scientist with a love of healthy baking, and this recipe is a great representation of how easy and delicious whole-wheat baking can be.
With a few tried-and-true techniques, you can make tall, tender and moist whole-wheat muffins! Let’s get into it.
This recipe article was originally published in April of 2021, it has since been updated with helpful tips, clearer instructions and step by step photos.
Reader Review
Beautiful muffin recipe! I doubled the recipe and for less sweetness used ⅓ c maple syrup because that’s what I had in hand. They turned out delicious! Moist, fluffy, a great texture. Thank you so much! Will absolutely make again.
– Natalia
Reader Review
Yummy and moist muffin. The spice level is perfect and ginger forward. Will work into my fall muffin rotation. Thanks ☺️
– Karen
Ingredients in Carrot Whole-Wheat Muffins
Here is a quick rundown of what you’ll need for the recipe. For ingredient amounts, jump down to the recipe card.
- Whole-wheat flour: regular or white whole-wheat work here.
- Cornstarch: a key ingredient in any whole-wheat baked good! Arrowroot starch will also work.
- Spices: ground ginger, cinnamon, nutmeg and kosher salt are what you’ll need.
- Leaveners: both baking powder and baking soda are needed for adequate lift.
- Greek yogurt: use plain whole milk Greek yogurt for the best flavor and texture.
- Olive oil: extra-virgin olive oil will add the best flavor. But melted coconut oil or even canola oil will work here.
- Honey: sweetens and keeps the muffins moist.
- Large eggs: make sure you use eggs labeled as “large.” One large egg, out of shell, should weigh 50 grams.
- Pure vanilla extract: pure extracts really do make a difference.
- Shredded carrots: shred the carrots yourself, either by hand using a box grater or with a food processor. Avoid using pre-shredded carrots from the store as the shreds are too large and won’t soften enough during baking.
- Pecans and turbinado sugar: for topping the muffin batter.
How to Make Healthy Carrot Muffins
This is an overview of the recipe, with step-by-step photos to guarantee success. Find the full recipe in the recipe card.
- Shred the carrots and set aside.
- Whisk together the whole-wheat flour, cornstarch, baking powder, baking soda, cinnamon, ginger and salt.
- In a separate bowl, whisk together the yogurt, oil, honey, eggs and vanilla.
- Add the dry mixture to the wet mixture and stir to combine.
TIP: one fabulous thing about baking with whole-wheat flour is that it develops gluten at a much slower rate than all-purpose flour. Therefore, you can’t really over-mix. So go ahead, mix the batter until it’s combined!
- Fold in the carrots using a rubber spatula.
- Divide the batter between paper-lined muffin cups. Sprinkle the tops with turbinado sugar and chopped pecans.
- Bake for 5 minutes at 425-degrees then drop temperature down to 350-degrees and bake until a toothpick inserted in the centers comes out clean.
TIP: starting the muffins at a high temperature will initiate a fast and tall rise, while dropping the temperature after five minutes will allow the muffins to cook through without burning.
- Let the muffins in the pan on a wire rack for 5 minutes, then remove muffins from pan and cool completely on wire rack. (Be sure to take the muffins out after 5 minutes. If they stay in the pan too long they will over-bake!)
Whole-Wheat Carrot Muffin Tips
- Cornstarch is a key ingredient in cake flour and/or cake recipes because it helps to create a tender crumb. It works the same here and does wonders for whole-wheat baking.
- The trick to getting a lovely domed muffin top (that we love about bakery muffins) is to jumpstart the baking at a high temperature in the oven (this activates the leavener). After a few minutes, drop the temp down to a medium heat (350ºF or 375ºF) to encourage even baking.
- Grease the inside of the paper muffin liners with oil or nonstick spray before adding the batter. This will make it so the muffins come out of the paper cleanly.
Storing and Reheating Carrot Yogurt Muffins
Store these muffins at room temperature, in an airtight container, for up to 2 days. After that, transfer them tot he fridge for up to 1 week.
The best way to reheat muffins is to place them in a 300ºF (148ºC) oven for 5–8 minutes. Alternatively, you can reheat them in a toaster oven.
For a quicker method, microwave them for 10–15 seconds. The only downfall of the microwave method is the muffin will become a but tough.
How to Serve Them
Round out the breakfast or brunch menu with my favorite Crustless Quiche and pair it all with a fun Fruit Salad.
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Ingredients
- 2 cups (240g) whole-wheat flour
- 2 tablespoons (18g) cornstarch or arrowroot starch
- 2 teaspoons ground ginger
- 1 ½ teaspoons ground cinnamon
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon kosher salt
- Heaping ¼ teaspoon nutmeg
- 1 cup (233g) plain whole-milk Greek yogurt*
- ⅓ cup (80g) extra-virgin olive oil or melted coconut oil
- ½ cup (180g) honey
- 2 large eggs (100g)
- 2 teaspoons (8g) pure vanilla extract
- 2 cups (178g) shredded carrots
- ¼ cup chopped pecans,
- 1 tablespoon turbinado sugar
Instructions
- Heat oven to 425°F (218°C). Line a 12-cup muffin tin with paper liners; coat liners with nonstick spray or oil.
- Whisk together 2 cups (240g) whole-wheat flour, 2 tablespoons cornstarch, 2 teaspoons ginger, 1 ½ teaspoons cinnamon, 1 teaspoon baking powder, ½ teaspoon baking soda, ½ teaspoon salt, and heaping ¼ teaspoon nutmeg in a medium bowl, set aside.
- Whisk together 1 cup (233g) Greek yogurt, ⅓ cup (80g) oil, ½ cup (180g) honey, 2 eggs, and 2 teaspoons vanilla in a large bowl until smooth.
- Add flour mixture to yogurt mixture and using a rubber spatula, mix until mostly incorporated but some pockets of flour remain. Gently fold 2 cups (178g) shredded carrots into batter.
- Divide batter (it will be thick) between prepared muffin cups, about ⅓ cup per muffin cup. Combine ¼ cup pecans and 1 tablespoon turbinado sugar and sprinkle evenly over cups of batter.
- Bake muffins 5 minutes at 425°F (218°C) then, keeping muffins in oven, reduce oven temperature to 350°F (177°C) and bake until a toothpick inserted in the centers comes out clean, 16–18 minutes more. (Total bake time is about 21–23 minutes.)
- Transfer muffin tin to a wire rack and cool 5 minutes, then transfer muffins from pan to wire rack to cool completely.
Yummy and moist muffin. The spice level is perfect and ginger forward. Will work into my fall muffin rotation. Thanks ☺️
Hey Karen! I’m so glad you enjoyed these, so perfect for fall! Thanks for letting me know how it went!
Hi, would this work with wholewheat pastry flour like in your “Healthy Lemon Blueberry Muffins” recipe?
Yes! I would measure the whole-wheat pastry flour by weight to get 240 grams (which should be about 2¼ cups). Let me know how it goes!
I have to stay Gluten-free, so no wheat for me..
Any alternative??
Hi Aileen—great question. I haven’t tested this, but I would recommend using Bob’s Red Mill GF flour blend or Cup for Cup. I would replace the wheat flour with either of these by weight—not by cup measure. I hope this helps!
Beautiful muffin recipe! I doubled the recipe and for less sweetness used 1/3 c maple syrup because that’s what I had in hand. They turned out delicious! Moist, fluffy, a great texture. Thank you so much! Will absolutely make again.
Hi Natalia, thanks for sharing your insights! This is so helpful for other readers. And I’m so glad you enjoyed these. Thanks for trying and thank you for leaving a review!
hello! thank you for this recipe! i cannot wait to make it!
a few questions…can i replace the whole wheat flour with almond flour? if so, what are the measurements? can i reduce the honey to 1/4 cup or even omit it?
Hi Cheryl!
Unfortunately almond flour is much heavier and denser than whole-wheat flour so it won’t work the same in these muffins. Almond flour also doesn’t have gluten, so it’s likely the muffins won’t rise as normal. I don’t recommend making that substitution. You can decrease the honey to 1/4 cup—the muffins may come out a bit less moist (and less sweet of course). I hope this helps!
Can u use maple syrup as sweetener?
Hi Hilary, great question. I haven’t tested this, so I can’t guarantee, but I think you’d have good luck with 1/4 cup maple syrup (in place of 1/2 cup honey). The muffins will be less sweet, but I worry if you use 1/2 cup maple syrup the batter will be too wet.
Another reader has had good luck using maple syrup—they doubled the batter and used 1/3 cup maple syrup for the double batch. But I think 1/4 cup maple syrup for a single batch would work fine. Let me know how it goes!
These sound great! Have you tested adding chia seeds or ground flax seeds to muffins to increase the fiber? Wondering if I’d need to adjust the recipe to ensure it has enough moisture.
Hi Natalie, great question. I haven’t tested this, but my first thought is you could replace the two eggs with 2 flax eggs, then you wouldn’t have to worry about moisture. My second thought, you could probably get away with adding a tablespoon of chia seeds to the batter without it impacting too much. If you want to add more than that, I would add 2 tablespoons milk for every 1 tablespoon ground flax, or 1 tablespoon milk for every 2 tablespoons chia seeds.
Flax egg:
For 2 large eggs, mix 14 grams (2 tablespoons) flax meal with 86 grams (6 tablespoons) water and let sit until thickened like a gel, 5–10 minutes. Use as directed in recipe.
I hope this helps! Let me know how it goes.
The best whole wheat muffins I’ve had! And the temp decreasing works for tall muffins!
Hi Jenna! So happy to hear you enjoy the muffins. Love that trick of starting at a high temp and then dropping it down to bake them through. Thanks for the comment and rating!
I baked these muffins today. The house smelled wonderful and the taste far surpassed my expectations. They are, without a doubt the most delicious healthiest carrot muffins I have ever tasted. Can’t thank you enough. I had to add a little sour cream to my yogurt to make enough but did no damage.
Hi Jane, wow, you just made my day! I’m so happy to hear you enjoyed these muffins. Great substitute with the sour cream, I may have to try that the next time I make these! I bet they were even better with that addition. Thank you for the comment!
Hi Lauren,
Would fresh ginger be an alternative to ground ginger powder here?
Thanks!
Hi Ushma! Yes, fresh would work great! And I think you could even keep the amount at 2 teaspoons. I may be more gingery, but delicious!
Is there a replacement for honey you’d recommend?
Yes! I would use 1/2 cup packed light brown sugar. Enjoy!
Can I sub maple syrup for the honey to make safe for baby?
Hi Jill, great question. I haven’t tested this, so I can’t guarantee, but I would swap the 1/2 of honey out for 1/4 cup maple syrup. The muffins will be less sweet, but I worry if you use 1/2 cup maple syrup the batter will be too wet.
Another reader has had good luck using maple syrup—they doubled the batter and used 1/3 cup maple syrup for the double batch. But I think 1/4 cup maple syrup for a single batch would work fine.
I hope you and baby enjoy these!
Absolutely delicious. Not sure if my scale is off but the weight vs measured was different, I used a scale for pretty much the whole recipe and they turned out perfect. Now to try the blueberry muffins and waiting for my home grown bananas to be ready for picking to make the banana bread!! Thanks for these recipes
Hi Vanda! Thanks for letting me know—I will recheck the weight vs measurements.
I can’t wait to hear what you think of the blueberry muffins and banana bread. If you’re looking for a good whole-wheat muffin, these are great (https://zestfulkitchen.com/healthy-whole-wheat-muffin-recipe/). I’m working on adapting them into a banana muffin as well!
I very rarely comment on recipes but these muffins are so good I have to! Well done Lauren best muffins I have ever made!
Laura! Get out of town, you just made my day!! So glad you enjoyed these 🙂
These are a STAPLE in my house. My picky 4 year old begs for carrot muffins. Thanks for a winning recipe that we keep stocked in my freezer at all times!
Nicole this is the best note!! I’m so glad your 4 year old enjoys these!
Hi Lauren,
This looks fabulous. I am going to try and make them today. Just a quick question. Does it have to be Greek yogurt? Can I use regular plain yogurt? Will it make a difference?
Lucy
Hi Lucy, apologies for the delay. Regular yogurt will add more moisture than Greek yogurt so you can do one of two things. The first option would be to decrease the total amount of yogurt down to 3/4 cup. The second option, which is a bit more involved but would likely be more effective, is to drain regular yogurt through a coffee filter for about 20 minutes. This will draw out excess moisture and essentially leave you with greek yogurt. I would start with 1 1/4 cups regular yogurt, drain it, then measure out 1 cup of the drained yogurt.
I hope this helps! I haven’t tested either of these methods, but this is where I would start. Let me know how it goes if you try either!
I made them and they were delicious but rather dry. I don’t think I over-mixed it. Can I add more oil to it next time? I love the taste. Or should I use regular yogurt instead of Greek?
Please advise. Thanks.
Hi Lucy, I’m sorry to hear they were dry! This surprises me because these muffins definitely lean into the “very moist” category with the carrots, oil and honey in the batter. Did you end up making the muffins with regular yogurt? And if so, did you decrease the amount you used or did you drain it? (Or neither?) This will help me pinpoint the issue.
Additionally, it’s very possible your oven runs hot, which is common. If you aren’t sure, I recommend getting an oven thermometer to test this. That way to can adjust your oven temperature as needed.
I made these muffins yesterday and they were delicious but very dry. I don’t think I over mixed it because I have made a lot of muffins before. Could it be that my oven is too hot? Should I use regular yogurt instead of Greek yogurt next time? Or increase the amount of oil?
It is a great recipe and I would like to try it again.
Hi Lucy, I know in your previous comment you mentioned wanting to use regular yogurt. I’m curious to know if you ended up using that and if you changed anything in the recipe because of it.
It’s very possible your oven runs hot, which is common. If you aren’t sure, I recommend getting an oven thermometer to test this. That way to can adjust your oven temperature as needed.
Secondly, whole milk greek yogurt (sometimes labeled as 5%) is important here because it has a fair amount of fat, which helps make the muffins moist. If you can, I recommend using that. Additionally, it’s possible too much flour was used. If you can, measuring out the flour by weight using a food scale is the most precise way to measure flour and ensures you don’t add to much. If you don’t have a good scale, it’s important to first fluff the flour with a spoon, then spoon the flour into the measuring cup, and finally level it off with a flat edge. Avoid “scooping” the flour with your measuring cup, as this packs the flour and thus adds more flour to the batter making the muffins dry.
Let me know if you have any questions!
Used all purpose instead of whole wheat and they were delicious. Definitely going to go on repeat.
thick like bread dough. some liquid is missing from the recipe . followed recipe exactly
Hi Kathy, I’m sorry to hear the batter came out too thick. As you can see in the video, the batter is quite thick—similar to carrot cake batter. But it certainly shouldn’t be thick like bread dough! I’ve tested this recipe many times and the finalized recipe I published should not have this issue. Do you remember why type of flour you used? I’m wondering if maybe too much flour was used. That’s really the only thing that I can think would cause this to be so thick. Is it possible too much flour was added? Thanks for your additional insights. I hope I can help you figure this out!
These turned out awesome!