This post may contain affiliate links. Please see our disclosure policy.
These Carrot Cake Muffins are deliciously spiced, perfectly tender, and filled with wholesome ingredients. Naturally sweetened, packed with whole grains, and dairy-free, these muffins let you enjoy the flavor of classic carrot cake without the sugar crash!
Looking for more muffin recipes that taste as decadent as dessert? Don't miss my recipes for Cranberry Orange Muffins, Oatmeal Chocolate Chip Muffins, and Chocolate Zucchini Muffins.
Kristen's Keys for Carrot Cake Muffins
To prevent dense muffins that lack flavor, pay attention to the following tips. They are the difference makers when it comes to making healthy swaps without sacrificing flavor or texture.
- Opt for whole white wheat flour. Still 100% whole grain, yet much lighter than traditional whole wheat flour. That lighter texture yields a light and tender muffin packed with fiber and whole grains.
- Sift dry ingredients together. While you could certainly just whisk the dry ingredients together, I find that sifting them together ensures a lighter crumb and no unpleasant clumps of baking soda or baking powder.
- Grate the carrots yourself. Store-bought grated carrots are much thicker and will not blend into the muffin like freshly grated carrots.
- Don't skip the crushed pineapple. Using crushed pineapple (and the juice leftover in the can) works to sweeten the muffins naturally and keep them moist.
How to Make Carrot Cake Muffins
Let me walk you through the process of making these whole wheat carrot cake muffins, with a few tips along the way.
Step One: Prepare Dry Ingredients
Over a large mixing bowl, sift flour, baking powder, baking soda, salt, cinnamon, nutmeg, and ground ginger together. Give the mixture a quick whisk to evenly distribute the ingredients.
Add the grated carrots (and chopped walnuts if using) and toss to coat the with the flour mixture. This helps prevent the carrots from sinking to the bottom of the muffin.
Step Two: Combine Wet Ingredients
To ensure not overworking the muffin batter, use a separate bowl to whisk the eggs, applesauce, oil, pineapple, honey, and vanilla together before adding them to the flour mixture.
Step Three: Combine Batter
Add wet ingredients to the flour mixture and gently fold together until just combined. Avoid mixing vigorously, which will make the muffins tough and dense.
Step Three: Portion out Muffins
Divide the batter evenly between lined or greased muffin cups. I like to use an ice cream scoop to keep the portions even and keep the mess to a minimum.
Step Four: Bake
Check on your muffins 5 minutes before the suggested cooking time, as all ovens bake differently and you don't want to overbake the muffins. You will know they are done when tops are set and a toothpick inserted into the center comes out mostly dry.
Recipe Modifications
- Gluten-Free: Use an all-purpose gluten-free flour blend in place of the flour. I have done this many times with success.
- Egg-Free: Replace the egg with a flax egg. Mix 1 tablespoon ground flaxseed with 3 tablespoons water, let sit for 5 minutes, then use in place of the egg.
- Swap out the Coconut Oil: Melted coconut oil adds a rich, nutty undertone to the muffin, but canola oil or melted butter can be used in its place.
- Optional Additions: Add up to ¼ cup chopped walnuts and ¼ cup raisins if desired.
- Ice the Muffins: Add a cream cheese frosting to the muffins to really replicate a classic carrot cake--icing and all!
Storage Tips
Keep in mind that muffins made with whole wheat flour should not be stored for more than a couple of days at room temperature, as they will quickly mold.
- To Store: Once the muffins have cooled to room temperature, store them in an airtight container at room temperature for up to 24 hours or in the refrigerator for up to 5 days.
- To Freeze: Place the cooled carrot cake muffins on a cookie sheet and flash-freeze for 30-60 minutes. Once the muffins are frozen solid, place them in a freezer-safe bag and store them in the freezer for up to 3 months. Defrost in the fridge overnight, or warm in the microwave for 1-2 minutes to heat before serving.
More Delicious Muffin Recipes
Carrot Cake Muffins
Video
Ingredients
- 1½ cups whole white wheat flour, or all-purpose flour
- 1 teaspoon baking soda
- ½ teaspoon table salt
- 1 teaspoon ground cinnamon
- ¼ teaspoon ground nutmeg
- ½ teaspoon ground ginger
- ¾ cup grated carrots, shredded on a box grater so that they are super fine
- ¼ cup chopped walnuts, optional
- ¼ cup raisins, optional
- ½ cup coconut oil, melted and cooled
- ⅓ cup honey, or maple syrup
- 1 teaspoon vanilla extract
- 1 large egg
- ½ cup unsweetened applesauce
- ½ cup canned crushed pineapple, not drained
Instructions
- Preheat the oven to 350℉ (175℃) and line a muffin pan with liners or grease well.
- In a large mixing bowl, whisk together 1½ cups whole white wheat flour, 1 teaspoon baking soda, ½ teaspoon table salt, 1 teaspoon ground cinnamon, ¼ teaspoon ground nutmeg, and ½ teaspoon ground ginger until well combined. Add in the ¾ cup grated carrots, and carrots and raisins if using. Toss to coat with flour.
- In a separate medium mixing bowl, whisk together ½ cup coconut oil ⅓ cup honey, 1 teaspoon vanilla extract, 1 large egg, ½ cup unsweetened applesauce, and ½ cup canned crushed pineapple.
- Add the wet mixture to the dry ingredients. Mix until just combined and the flour is moistened fully, being careful to not overmix. The batter will be thick!
- Scoop with an ice cream scoop or ¼ cup measuring cup into the prepared muffin tin.
- Bake for 20-25 minutes, or until a toothpick inserted into the center comes out dry.
- Cool muffins for 10 minutes on a cooling rack in the muffin tin and then remove muffins and cool completely on the rack.
Equipment
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
This post was originally published in 2019 and updated in 2026.
I am always looking for healthier baked goods recipes and this one is a winner! These muffins are so tasty and easy to make. My kids love them!
YAY! I love hearing your family enjoyed Anna!
So delicious!
Followed the recipe as is except I omitted the walnuts and loved it. Great recipe!
I am so glad you enjoyed Sarah!
I never bake anymore due to many poor outcomes but I have a new convection oven and this looked good so I tried it and it was wonderful. Easy to put together and I made only 6 muffins and a small loaf of bread. I just cooked it another 10 minutes longer. I had a fresh pineapple so made my own 'crushed'. Used powdered ginger.
YAY! I am so glad that you had success with this recipe and your new oven.
Hi! This recipe looks great! I was just wondering about the ginger. Powder or grated?
Thanks!
Hi Rupi, for this recipe is it powdered ginger.
Store-bought muffins are filled with sugar.. I love that this is a healthy version of muffins! I feel good about serving them to my family, Delicious.
So glad you enjoyed these healthier muffins!
My youngest loves carrot cake. Will totally have to make this for him. Thank you for sharing.
I hope you enjoy!