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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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Healthy Carrot Muffins
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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.
Is the cornstarch absolutely necessary or can I omit? Thank you!
Hi Stephanie, cornstarch helps the crumb of the muffin stay light and tender. You can skip it, just know the texture might be a little less airy and “cakey.” Substitute with an additional 1 tablespoon whole-wheat flour.