Made with whole wheat flour and naturally sweetened, these Healthy Carrot Cake Muffins are light, fluffy, and full of incredible flavor.

Just like my recipe for Healthy Blueberry Muffins and Chocolate Zucchini Muffins, this recipe for Healthy Carrot Cake Muffins compromises nothing in taste or texture, yet is made with wholesome ingredients.

Muffin tray with baked muffins and one carrot cake muffin cut in half to side of tray revealing carrots and raisins inside muffin.

If you love classic carrot cake, made with shredded carrots, pineapple, and nuts, you will LOVE this recipe for Healthy Carrot Cake Muffins.

These whole wheat muffins are perfectly spiced and reminiscent of rich, decadent carrot cake, yet made with wholesome ingredients. And don't worry, these healthy swaps do not compromise the flavor or texture of these muffins. They are light, fluffy, and simply delicious.

what makes these carrot cake muffins healthy

Naturally Sweetened: Instead of adding 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. And 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. Carrot cake muffins are made with whole wheat flour, carrots, and raisins, which add a healthy dose of fiber, not to mention vitamins A and B and iron.
Dairy-Free. These muffins are made without butter or milk, therefore they are the perfect treat for anyone with a dairy allergy.

Notes On Ingredients

Ingredients for Carrot Cake Muffins on counter.

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. Whole white wheat flour 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 them.
Nuts: Use chopped walnuts or pecans, or omit the nuts altogether.

Tips for Making Healthy Carrot Cake Muffins

This recipe for carrot cake muffins comes together easily, and you will find detailed instructions in my recipe card. However, I do want to walk you through a few expert tips to ensure your muffins turn out fluffy, moist, and delicious.

Tip #1: Use silicone muffin tin liners. I love to use silicone muffin liners when making homemade muffins because the batter does not stick to the liner, as it does if you were to use a paper muffin liner, meaning more carrot cake muffins for you to enjoy!

Tip #2: Toss the carrots, raisins, and nuts with flour. After whisking together the dry ingredients together, add the shredded carrots, raisins, and nuts directly to the flour mixture and toss them in the flour to coat. By coating these additions in flour, you will help to ensure that they are all evenly disbursed through your muffins, making each bite as delicious as the first!

ingredients for carrot cake muffins on white counter. One bowl with dry ingredients one glass bowl with wet muffin ingredients

Tip #3: Don't over-mix the muffin batter. Add wet ingredients to the flour mixture and stir until just combined, or until the flour is fully moistened. If you mix the batter too vigorously, the muffins will become tough and dense.

Tip#4: Use an ice cream scoop to keep the muffins even in size. In order for the muffins to bake evenly, each muffin needs to be about the same size. I find that about ¼ cup of muffin batter per muffin cup is the perfect amount of batter. I love using an ice cream scoop to scoop out the muffin mixture into the muffin liners, as it is the perfect amount needed and helps to prevent a mess.

Tip #5: Bake until just set. 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. They will be done when the tops of the carrot cake muffins are set and a toothpick inserted into the center comes out dry.

12 carrot cake muffins in silicone muffin liners in 12 cup muffin tin.

How to Store Carrot Cake Muffins

Once the muffins have cooled to room temperature, store them in an airtight container. Because these carrot cake muffins are made with whole wheat flour and without preservatives, they need to be refrigerated or frozen if not consumed within two days of baking.

To Refrigerate: Carrot cake muffins will last 5 days when stored in an airtight container in the refrigerator.
To Freeze: Place the cooled carrot cake muffins on a cookie sheet and freeze for 30-60 minutes until solid. That process helps prevent the muffins from sticking together when frozen. 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.

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

If you enjoyed these easy, wholesome, carrot cake muffins, I would love for you to leave a comment and review below.