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-packed Greek yogurt. A handful of warm spices and a sweet-crunchy topping secure these in the breakfast hall of fame. 

carrot muffin with a bite taken out of it set on a table with a pat of butter on top and honey dripping off it

Ingredients Needed

  • whole-wheat flour—you can also use white whole-wheat flour.
  • cornstarch—arrowroot starch will also work.
  • spices— ground ginger, cinnamon, nutmeg and kosher salt.
  • leaveners— baking powder and baking soda.
  • Greek yogurt—I recommend using whole milk Greek yogurt, but you can use whatever fat percentage you prefer.
  • extra-virgin olive oil—you can also use regular olive oil or melted coconut oil.
  • honey—I always prefer to use honey instead of brown sugar. It’s less processed and has more flavor!
  • Large eggs—make sure you use eggs labeled as “large.”
  • Pure vanilla extract—pure extracts really do make a difference.
  • shredded carrots—shred the carrots yourself, either by hand or with a food processor. Avoid using pre-shredded carrots from the store as the shreds are too large.
  • Pecans and demerara sugar—these are for the topping and are optional, but recommended! You can use turbinado sugar in place of the demerara sugar.
olive oil, honey, shredded carrots, flour, spices, yogurt, and vanilla measured out in bowls. Eggs arranged around bowl

How to Make Healthy Carrot Muffins

  1. Read through the recipe and make sure you have everything you need!
  2. Preheat the oven.
  3. Shred the carrots. I recommend shredding the carrots by hand or with a food processor with the grater attachment. Store-bought shredded carrots are too large.
  4. Whisk together the dry ingredients in a medium bowl.
  5. Whisk together the wet ingredients in a large bowl.
  6. Add dry ingredients to wet ingredient and mix until mostly combined but some pockets of flour remain. 
  7. Fold in the carrots.
  8. Divide between muffin cups then sprinkle tops with demerara sugar and pecans.
  9. 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.
  10. Cool muffins in pan on 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!)
collage of three images showing how to mix up a muffin batter, adding shredded carrots to batter, and scooping batter into muffin tin

Tips for Making Delicious Healthy Muffins 

  1. Add Cornstarch: 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.
  2. Make Intentional Ingredient Substitution: swap traditional ingredients that are both healthier and more flavorful. For example, instead of vegetable oil, use a robust extra-virgin olive oil. Instead of regular sugar, use a floral honey. Instead of milk, add buttermilk for some tang or Greek yogurt for tang and protein.
  3. Start Baking at a High Temperature: 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.
  4. Add Some Crunch: it’s always my goal to create a healthy muffin that’s tender. The best thing to pair with that tenderness? Crunch! Sprinkle something crunchy—raw sugar, nuts, oat crumble—over each well of batter right before baking. This will create a lovely crunchy muffin top!
muffins in a muffin tin with pecans scattered around and butter set next to it

How Long Do Carrot Muffins Last?

Stored at room temperature, lemon blueberry muffins will keep for two days. Stored in an airtight container in the refrigerator, these muffins will last for up to 1 week.

How to Reheat Muffins

I prefer the quick microwave-method for reheating muffins. They don’t need much time, just 10–15 seconds. The only downfall of the microwave method is the muffins tender to get a bit tough in texture. You can also reheat muffins in a 300ºF (148ºC) oven until warmed through, 5–8 minutes. 

muffins stacked in a muffin tin


  • Make these “carrot cake muffins” by adding some shredded coconut or raisins in place of some of the carrots. Drizzle a cream cheese frosting over muffins once they’ve baked and cooled.
  • Top with an oat crumble instead of the sugar and pecan combo.
  • Make a carrot bread! Check out our favorite Whole-Wheat Browned Butter Carrot Bread

Make It a Meal, Serve Muffins With…

muffins in a muffin tin with pecans scattered around and butter set next to it

If you make this Healthy Carrot Muffin recipe be sure to let me know! Leave a comment with a star rating below. You can also snap a photo & tag @zestfulkitchen on Instagram. I love hearing about and seeing your ZK creations!

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muffins stacked in a muffin tin

Healthy Carrot Muffins

  • Author: Lauren Grant
  • Prep Time: 15 minutes
  • Cook Time: 25 minutes
  • Total Time: 40 minutes
  • Yield: 12 standard muffins 1x
  • Category: Breakfast
  • Method: Baking
  • Cuisine: American
  • Diet: Low Fat


Tender, perfectly sweet and lightly spiced, these carrot muffins are the ultimate healthy breakfast or snack! Made with whole-wheat flour, carrots, olive oil, Greek yogurt and honey, these muffins are wholesome through-and-through!


  • 2 cups whole-wheat flour (8.5oz.; 240g)
  • 2 tablespoons cornstarch or arrowroot starch (18g)
  • 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 plain whole-milk Greek yogurt* (233g)
  • ⅓ cup extra-virgin olive oil, or melted coconut oil (80g)
  • ½ cup honey (180g)
  • 2 large eggs (100g)
  • 2 teaspoons pure vanilla extract (8g)
  • 2 cups shredded carrots (178g)* 
  • ¼ cup chopped pecans, optional
  • 1 tablespoon demerara sugar (sugar in the raw), optional


Heat oven to 425°F (218°C). Line a 12-cup muffin tin with cupcake liners (or grease the cups with nonstick cooking spray).

Whisk together flour, cornstarch, ginger, cinnamon, baking powder, baking soda, salt, and nutmeg in a medium bowl, set aside.

Whisk together yogurt, oil, honey, eggs, and 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 shredded carrots into batter.

Divide batter (it will be thick) between prepared muffin cups, about ⅓ cup per muffin cup. Combine pecans and demerara 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.

Store cooled muffins at room temperature in an airtight container for up to 2 days, or in the refrigerator for up to 5 days.

Reheat muffins in the microwave for 10–15 seconds or reheat in a 300-degree oven for 5 minutes. 


Carrots: You’ll need about ¾ lb. of carrots to get 2 cups shredded. 

*Greek yogurt: I recommend whole-milk Greek yogurt, but you can use any fat content you prefer, just be sure to use Greek yogurt. Sour cream can also be substituted. 

Bake by internal temp: checking internal temperature is a great way to determine whether or not the muffins are ready. Insert the probe of an instant-read thermometer into the center of a muffin, if it temps 206–210ºF they are ready to be pulled out of the oven!


  • Serving Size: 1 muffin
  • Calories: 200
  • Sugar: 14g
  • Sodium: 127mg
  • Fat: 7.5g
  • Saturated Fat: 1.5g
  • Carbohydrates: 29g
  • Fiber: 3g
  • Protein: 5g
  • Cholesterol: 33mg

Keywords: healthy carrot muffins, carrot muffins, healthy muffins

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About The Author

Lauren Grant is a professional culinary food scientist, food writer, recipe developer, and food photographer. Lauren is a previous magazine editor and test kitchen developer and has had work published in major national publications including Diabetic Living Magazine, Midwest Living Magazine, Cuisine at Home Magazine, EatingWell.com, AmericasTestKitchen.com, and more.

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  1. Yummy and moist muffin. The spice level is perfect and ginger forward. Will work into my fall muffin rotation. Thanks ☺️

  2. Hi, would this work with wholewheat pastry flour like in your “Healthy Lemon Blueberry Muffins” recipe?

    1. 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!

    1. 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!

  3. 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.

    1. 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!