Made with 100% whole grains and naturally sweetened, these Carrot Cake Muffins are healthy, yet bake up light and fluffy and are full of incredible flavor thanks to the addition of shredded carrots, plump raisins, crunchy walnuts, and sweet pineapple.

Carrot Cake Muffins has been given a make-over!
With a few healthy swaps, this recipe for Carrot Cake Muffins produces a muffin that is lower in fat, sugar, and full of nutrients, yet tastes 100% delicious!
- Naturally Sweetened: Instead of adding in refined sugars, these Carrot Cake Muffins are sweetened with a small amount of honey. Raisins, crushed pineapple, and applesauce also add to the sweetness of these muffins naturally.
- 100% Whole Grain. Instead of refined all-purpose flour, this recipe calls for whole wheat flour. While most whole wheat baked goods have the reputation of being dense, the addition of coconut oil and applesauce keeps these muffins light and tender.
- Packed full of Nutrients. Whole wheat flour, carrots, and raisins add a healthy dose of fiber, not to mention vitamins A and B and iron, and walnuts add healthy fats and omega-3 fatty acids.
- Dairy-Free. These muffins are made without butter or milk, therefore they are the perfect treat for anyone on a dairy-free diet.
The healthy swaps did NOT compromise the flavor or texture of these muffins. These Healthy Carrot Cake Muffins are perfectly spiced and reminiscent of rich, decadent carrot cake, yet made with wholesome ingredients. They are absolutely delicious.
Notes On Ingredients

- Carrots: It is best to grate the carrots yourself, rather than purchasing grated carrots. Store-bought grated carrots are much thicker and will not blend into the muffin as well as freshly grated carrots.
- Flour: For best results, use whole white wheat flour. It is still 100% whole grain, but yet produces a lighter crumb than traditional whole wheat flour.
- Crushed Pineapple: Use canned crushed pineapple that has been canned in 100% juice. There is no need to drain the pineapple, as the moisture will help keep the muffins tender and moist.
- Coconut Oil: Feel free to use canola oil in place of coconut oil. I prefer the taste of coconut oil to canola oil in baked muffins, but either oil will work.
- Honey: Feel free to use maple syrup in place of the honey if desired.
- Applesauce: Be sure to use unsweetened applesauce to keep these muffins low in added sugar.
- Raisins: It is debatable whether raisins are traditional in carrot cake. Some recipes call for them, some do not. I personally love the burst of sweetness and texture they add to the muffins but feel free to omit.
- Nuts: Use chopped walnuts or pecans, or omit the nuts altogether.
How to Make Carrot Cake Muffins
- Grease a 12 cup muffin tin or line with silicone muffin liners.
- Mix together dry ingredients in a large mixing bowl until everything is well incorporated. You want to be sure the baking soda and spices are evenly distributed throughout the flour.
- Add in carrots, raisins, and nuts and toss well to coat with flour. By coating these additions in flour, this step helps all those goodies to not sink to the bottom of the muffins.
- In a separate bowl, whisk together the applesauce, coconut oil, eggs, pineapple, and vanilla extract.

- Add wet ingredients to the flour mixture and stir until just combined, or until the flour is fully moistened. Do not over mix or you will have a tough and dense muffin!
- Scoop about ¼ cup batter into each muffin tin. Pro-tip: Use an ice cream scoop to scoop out the muffin mixture into the muffin liners. It is the perfect amount needed and helps to prevent a mess.
- Bake until muffins are set and a toothpick inserted into the center comes out dry.
- Cool the muffins in the muffin tin for 10 minutes and then remove the muffins from the pan and allow to cool fully on a cooling rack.

How to Store Carrot Cake Muffins
Once the muffins have cooled to room temperature, store them in an airtight container. If not consumed within 2 days, it is best to refrigerate the muffins.
When baking with whole grain products, it is best to refrigerate or freeze whole wheat muffins, or any whole wheat products, after they are cooled to room temperature if not consumed within 2 days.
You can also freeze the muffins for up to 3 months. Place muffins on a cookie sheet and freeze for 30-60 minutes until solid--this process helps muffins not stick together when placed in a container in the freezer. Then place in a freezer-safe bag and pull one muffin out at a time. Defrost in the fridge overnight, or warm in the microwave for 1-2 minutes to heat before serving.
Recipe Modifications
- Gluten-Free Carrot Cake Muffins : Use an all-purpose gluten-free flour blend in place of the flour. I have done this many times with success.
- Egg Free Carrot Cake Muffins: Replace the egg with a flax egg. Mix together 1 tablespoon ground flaxseed with 3 tablespoons water, let sit for 5 minutes, then use in place of the egg.
- Nut-Free Carrot Cake Muffins: Omit nuts if desired/needed
More Healthy Muffin Recipes
- Whole Wheat Pumpkin Muffins
- Double Chocolate Zucchini Muffins
- Gluten-Free Cinnamon Streusel Muffins
- Cinnamon Applesauce Muffins
- Healthy Blueberry Muffins
If you enjoyed these simple carrot cake muffins, I would love for you to leave a comment and review below.

Healthy Carrot Cake Muffins
Ingredients
- 1 ½ cups whole wheat flour
- 1 tsp baking soda
- ½ tsp salt
- 1 tsp cinnamon
- ½ tsp freshly grated nutmeg
- ½ tsp ginger
- ¾ cup grated carrots
- ¼ cup raisins
- ¼ cup chopped walnuts
- ½ cup melted coconut oil measure and then heat to melt
- ⅓ cup honey
- 1 tsp vanilla
- 1 egg
- ½ cup applesauce
- ½ cup crushed pineapple not drained
Instructions
- Preheat oven to 350 and line a muffin pan with liners or grease well.
- In a large mixing bowl, combine the flour, baking soda, salt, cinnamon, ginger, and nutmeg until well combined. Add in the carrots, raisins, and nuts and toss to coat with flour.
- In a separate smaller mixing bowl, mix together the oil, vanilla, egg, honey, applesauce, and pineapple until combined. Add to dry ingredients. Mix until just combined or the flour is moistened fully. The batter will be thick!
- Scoop with an ice cream scoop or ¼ cup measuring cup into the 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 Needed
Notes
Nutrition
This recipe has been updated in 2021 with a few new tips, but the recipe remains the same.
LAUREN KELLY
My absolute favorite muffins. And the best part is my kids love them too!
Kristen Chidsey
I am so glad you and your kids enjoyed Lauren!
Anna
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!
Kristen Chidsey
YAY! I love hearing your family enjoyed Anna!
Katie
So delicious!
Sarah
Followed the recipe as is except I omitted the walnuts and loved it. Great recipe!
Kristen Chidsey
I am so glad you enjoyed Sarah!
Jeanne Watkins
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.
Kristen Chidsey
YAY! I am so glad that you had success with this recipe and your new oven.