carrot muffins
Desserts,  Breakfast,  Snacks

Carrot Cake Muffins (Healthy + Gluten-Free)

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Fluffy, slightly chewy, and so moist! These Healthy Carrot Cake Muffins are insanely good while still being oil-free, gluten-free, refined sugar-free, grain-free, and paleo! They’re the perfect breakfast muffin, toddler snack, or holiday dessert!

carrot cake muffins
healthy carrot muffins

Are Carrot Muffins Healthy?

Most carrot cake muffins are NOT healthy. You think carrot cake or carrot muffins would be healthy because they have that orange veggie in them right? However, most carrot muffins are loaded with processed sugar and flour. 

Don’t worry, there is hope! In this recipe, we use very different ingredients to make these muffins low glycemic, lower in sugar, paleo, grain-free, oil-free, gluten-free and vegan friendly. Let’s jump into the healthy ingredients below. (figuratively)

carrot muffins with cream cheese frosting
carrot muffin recipe

How to Make Carrot Muffins

These carrot cake muffins are super easy to make! You only need one bowl and either a box grater or food processor. See my recommendations for those kitchen utensils below. First, let’s start with the ingredients you’ll need.

Only 9 key ingredients!

  • Eggs
  • Coconut Sugar
  • Spices: Cinnamon, Ginger, Nutmeg, Salt
  • Plant Based Milk
  • Coconut Flour
  • Almond Flour
  • Tapioca Flour (or cornstarch) 
  • Carrots
  • Baking Powder & Baking Soda
healthy carrot muffins
carrot breakfast muffins

Healthy Carrot Cream Cheese Muffins

I love adding a healthy cream cheese frosting to the top of my carrot muffins. I use this cream cheese icing in so many of my healthy recipes. You can find it hanging out on my Healthy Carrot Cake, Healthy Sugar Cookies, Vegan Sugar Cookies, or my Gluten-Free Sugar Cookies

The cream cheese icing we use is just 3 ingredients and can easily be made dairy-free by using vegan cream cheese.

healthy Easter dessert
healthy carrot cake cupcakes

How to Shred Carrots

There are two main options when it comes to shredding carrots.

  1. Peel carrots, then shred using a box grater.
  1. Peel carrots, then place in a food processor with the grater attachment. (here is the food processor I use that comes with a grater attachment)

I chose the later of the two because it is just so easy! Here are a couple step by step videos for how to shred a carrots by hand and how to shred carrots in a food processor.

Moist Carrot Cake Muffins

I went over my top 3 secrets to making THE BEST healthy muffins in my Healthy Banana Chip Muffins recipe so you’ll definitely want to check that out.

Overall, what gives these carrot muffins that moist texture is:

#1 the shredded carrots

#2 the lovely gluten-free flour combo we use

Almond flour, tapioca flour, and coconut flour makes for the fluffiest, yet most melt in your mouth gluten-free muffins! If you’re more of a whole wheat type of person (or if you don’t have those fancy flours), my Healthy Pumpkin Muffins would be the perfect recipe for you!

moist carrot cake muffins
Picture evidence of how moist they are!
moist carrot cake cupcakes

Carrot Breakfast Muffins

These carrot cake muffins are so healthy that you can actually eat them for breakfast! The nutrition information is listed at the end of the recipe to prove it. They’re only 152 calories and have 50.4% of your daily calcium intake and 317.8 mg of potassium! 

Talk about a delicious, easy, on-the-go breakfast idea! I love meal prepping these muffins and storing them in an airtight container in the fridge to grab and go on my busy days. I’m sure you  can relate to this.

carrot cake muffins

Toddler and Baby Approved Carrot Muffins!

Speaking of busy days… these muffins are the perfect snacks for your kids! Toddlers and babies are able to eat these muffins and trust me, they will love them! Plus, you as a mama, can feel GOOD giving them these carrot muffins because you know what’s in them and how they are nourishing your little ones. Win, win!

What to Add to Carrot Cake Muffins

The possibilities are endless when it comes to optional add-ins for these muffins. Here is a list of delicious possible ingredients you can add to your carrot muffin batter:

  • Apple
  • Pineapple
  • Walnuts
  • Coconut
  • Raisins
  • Chocolate Chips

I cannot wait for you to give these carrot cake muffins a try! Please snap a picture and share it with me! 

Seeing your kitchen creations makes my day and encourages me to keep creating new recipes for you!

Happy Muffin Makin’!


paleo carrot muffins
Yield: 7 Muffins

Carrot Cake Muffins (Healthy + Gluten-Free)

carrot muffins

Fluffy, slightly chewy, and so moist! These Healthy Carrot Muffins are insanely good while still being oil-free, gluten-free, refined sugar-free, grain-free, and paleo! They’re the perfect breakfast muffin, toddler snack, or holiday dessert!

Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes




Cream Cheese Frosting

  • ½ Block Cream Cheese (you can use low fat or vegan)
  • ¼ Cup Powdered Sugar
  • ½ -1 Tbs Plant Based Milk


1. Preheat oven to 350 F. and line a muffin tin with silicone muffin liners, paper liners, or grease with coconut oil.

2. In a medium bowl, combine all the wet ingredients and whisk until smooth.

3. To the wet mixture, fold in the coconut flour, tapioca flour, and almond flour.

4. Lastly, fold in the shredded carrots, baking powder, and baking soda.

5. Divide the batter evenly among muffin tins, filling each almost to the top (should fill 7 muffin cups).

6. Bake at 350 F. for 19-23 minutes until a toothpick comes out clean or with just a few moist crumbs attached. Opt: While the muffins bake, make the cream cheese frosting.

7. Let cool for 5 minutes before transferring muffins out of pan. Opt: Top with homemade cream cheese frosting.

8. Store in an airtight container in the fridge for a week or freeze for up to 3 months.

For the Frosting:

Combine softened cream cheese, powdered sugar, and plant based milk in a medium bowl. Beat with a hand mixer or standing mixer until smooth.


  1. To make these carrot muffins vegan: swap the eggs for 2 flax eggs. Check out my Vegan Raspberry Brownie Recipe for a step by step of how to make these (chia eggs are the same ratio and instructions).
  2. Don't have tapioca flour? You can use ¼ cup cornstarch instead! It’s not an even 1:1 swap so be sure you only add ¼ cup not ½ cup.

Be sure to tag @secretlyhealthyhome on Instagram, Facebook or Pinterest with a picture of your muffins!

I love seeing your kitchen creations so please leave a comment and rate the recipe if you make it! It really helps support me and encourages me to keep making recipes for you!

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Nutrition Information:



Amount Per Serving: Calories: 152Total Fat: 4gCarbohydrates: 27.4gNet Carbohydrates: 23.4gFiber: 4gSugar: 18.6gProtein: 3.6g

Did you make this recipe?

Be sure to tag @secretlyhealthyhome on Instagram, Facebook or Pinterest with a picture of your recipe creation! Please leave a star rating and or comment! It really helps support me and encourages me to keep making recipes for you!

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  • Betsy Richmann

    I made these for Easter brunch and they were a hit! Just as the recipe says they are soft, moist, and a little chewy! They’re excellent with the frosting or just dusted with powdered sugar! I’ll definitely be making these again!

    • Claire

      So glad you and your family enjoyed them! Such a perfect treat for Easter. Love it! Thank you Betsy! 🙂

    • Claire

      Hi! They have about 27 carbs per muffin, so I would not consider them low carb 🙂 They are high in nutrients and low glycemic though so they won’t spike your blood sugar.

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