Carrot Cake Cupcakes Recipe - Dr. Axe

Carrot Cake Cupcakes Recipe

Carrot cake cupcakes recipe - Dr. Axe

Just because the word “carrot” is in the name, doesn’t mean that carrot cake is a healthy option for dessert. Well, at least not always. My carrot cake cupcake recipe includes beneficial alternatives for the typical, not-so-healthy ingredients in carrot cake.

I use gluten-free flours in my carrot cake and natural sugars; plus, it’s topped with my all-natural and organic cream cheese frosting.

When eating these cupcakes, you can actually feel like you’re doing something good for your body. And you aren’t counteracting the benefits of carrots (like their ability to protect your eyesight and brain function) with pro-inflammatory flour and sugar.

Key Ingredients

Many carrot cake recipes call for white sugar, white flour and canola oil — ingredients that I choose not to use in my desserts. The truth is that you can stick to healthy ingredients without forfeiting the taste. These carrot cake cupcakes prove just that.

I use two gluten-free flours in my carrot cake cupcakes: almond flour and coconut flour. Almond flour is made from almonds and only almonds, which are blanched to remove the skin and then ground. Instead of using an ingredient like white flour, that could be detrimental to your health, why not choose a flour that will promote your well-being and supply vitamins and minerals like vitamin E, iron, magnesium, potassium and calcium?


Just like almond flour, coconut flour is gluten-free, which is important to me because gluten can irritate the gut, which we know can lead to a slew of health issues. Coconut flour is high in fiber, so its components move through the digestive tract quickly, taking toxins and waste with them.

I also choose to use coconut oil instead of canola oil in my healthy carrot cake cupcakes. I don’t like to use canola oil because it’s a refined, genetically modified product that can cause a number of health issues.

Coconut oil, on the other hand, helps to prevent heart disease and high blood pressure, and it works to protect the liver and kidneys.

How to Make Carrot Cake Cupcakes

Now that we know healthy carrot cake recipes do exist, let’s get into baking these delicious cupcakes. Before you get your batter prepared, preheat your oven to 350 degrees F.

In a large mixing bowl, begin to add your ingredients. I start with the dry ingredients first: almond flour, coconut flour, baking soda, cinnamon and ground ginger.

The cinnamon and ginger really enhance the flavor of these carrot cake cupcakes. And, in case you didn’t know, ginger health benefits include its ability to help relieve indigestion and boost the immune system with its powerful antioxidant and anti-inflammatory properties.

Instead of sugar, I use maple syrup, which is a great alternative when used in small amounts. The glycemic index score of maple syrup is about 54, compared to a score of 65 for regular cane sugar.

After you add your maple syrup to the dry ingredients, add the remainder of your wet ingredients, eggs, coconut oil and vanilla extract.

Allow the mixture to sit for 5 minutes so that it all comes together and then fold in ½ cup of grated carrots.

Add the mixture to a lined or oiled muffin pan and bake them for 18–20 minutes. This recipe should make about 12 cupcakes.

Let your muffins cool off when they come out of the oven and then make up the cream cheese frosting.

I make my cream cheese frosting with four simple ingredients: organic cream cheese, coconut milk, maple sugar and coconut flakes. Using a high-powered mixer, mix these four ingredients together until well-combined.

Your carrot cake cupcakes are done and ready to enjoy!


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Carrot cake cupcakes

Carrot Cake Cupcakes Recipe

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  • Author: Dr. Josh Axe
  • Total Time: 35 minutes
  • Yield: 12 cupcakes 1x
  • Diet: Gluten Free


My carrot cake cupcake recipe includes beneficial alternatives for the typical, not-so-healthy ingredients in carrot cake. And the results are delicious!




  • 1¼ cups almond flour
  • 2 tablespoons coconut flour
  • ½ teaspoon baking soda
  • 2 teaspoons cinnamon
  • 12 teaspoons ground ginger
  • 2 eggs
  • ⅓ cup coconut oil
  • ⅓ cup maple syrup
  • 2 teaspoons vanilla
  • ½ cup grated carrots

Cream Cheese Frosting

  • 8-ounce package grass-fed, organic cream cheese
  • ¼ cup evaporated coconut milk or coconut milk
  • 2 tablespoons maple sugar
  • ½ cup unsweetened, shredded coconut flakes


  1. Preheat oven to 350 F.
  2. in a large mixing bowl, add all the ingredients, except the carrots, mixing until well combined.
  3. Allow mixture to sit for 5 minutes.
  4. Fold in the carrots.
  5. Add mixture to a lined or oiled muffin pan.
  6. Bake for 18–20 minutes.
  7. While the cupcakes bake, make up the cream cheese frosting. Using a high-powered mixer, mix all ingredients together until well-combined.
  8. Top with cream cheese frosting.
  • Prep Time: 15 min
  • Cook Time: 20 min
  • Category: Desserts, Snacks
  • Method: Baking
  • Cuisine: American


  • Serving Size: 1 cupcake (71g)
  • Calories: 253
  • Sugar: 8.4g
  • Sodium: 152mg
  • Fat: 21.3g
  • Saturated Fat: 11.7g
  • Unsaturated Fat: 8.4g
  • Trans Fat: 0g
  • Carbohydrates: 12.6g
  • Fiber: 2.5g
  • Protein: 5.4g
  • Cholesterol: 44mg

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  1. Robin on

    I would like to try these as they sound yummy… But recently found out I’m sensitive to coconut ( having to rearrange my life as coconut was everywhere in my diet). I can sub the coconut oil for avocado – could I sub out the coconut flour with cassava? Thanks

  2. tom on

    This post is so useful, I have looked all over the internet for it, thank you so much for sharing it. The article is so clear, without this post, I won’t be able to understand its use.
    mc wiki

  3. Margie Teraoka on

    I love these cupcakes! They are my favorite dessert recipe from Dr Axe. I add either pecan or walnut pieces for added flavor. These can be frozen, unfrosted. Thaw at room temp and frost. His cream cheese frosting recipe is perfect to top them with.

  4. Brigitte Nelson on

    This looks and sounds delicious. What can I use for a non dairy option for the cream cheese? My son is gf/DF!

    • Ethan Boldt on

      You can but probably a mix of stevia and monk fruit would work best, if you want to avoid all sugar and also get a good flavor.

  5. Julie on

    Sounds great.
    If I wanted to double the recipe is that ok or are there any changes that would need to be done? Some recipes you can’t just double each ingredient

    Can you add raisins and zucchini too?

    Thank you

  6. Ida on

    Hi Dr. Axe, I listen to you religiously.

    Kindly give us a recipe for a carrot cake or carrot balls without sugar, without baking. Thanks
    In Yugoslavia I used to make carrot balls and take them to the mountain when skiing but they were with sugar

  7. Peggy on

    Hey Dr Axe I tried the carrot cake cupcakes and I liked them so o o o o much. I ate three without the cream cheese frosting. They were very moist. I used raw honey as the sweetener. Now I have to exercise for an hour. Thanks

  8. Kerstin on

    Loved these! Kid friendly too. I actually made them without the “cream cheese” frosting. My picky daughter likes them! Thank you.

  9. Adriona Carr on

    I was just wondering could I swop out the almond flour , for chick pea flour. I have a family member that’s allergic to all tree nuts and peanuts, accept for cashews.

  10. Joseyjane Roberts on


  11. Josephine on

    You say “mix”, do you just mix the ingredients with a spoon? No need to use the mixer? If not, that would be awesome.

  12. Charlotte on

    yuuuuummmmmm. Thanks heaps doc. This is amazing.
    Also thankyou for all the awesome work you do. Ive been a follower of your for some time now and just love EVERYTHING you do. So thanks again from Australia :)

  13. Peter on

    Great recipe that inspires me to give it a try, and I would love to move the ingredients to be a little more Keto if possible. I grow my own ginger and coconuts and will experiment using fresh rather than dried ingredients. Do you have the nutritional break down on what the current recipe produces?

    • Dr. Josh Axe on

      Hi Peter, here are the nutrition facts for the recipe as is: 136 calories, 9 grams carbs, 11 grams fat, 4 grams protein, 71 grams sodium and 4 grams sugar. I hope this helps!

    • Dr. Josh Axe on

      Here are the egg substitutions I recommend: One egg = ½ mashed banana, ¼ cup applesauce, 1 tablespoon ground flaxseed meal + 3 tablespoons water; 1 tablespoon chia + 3 tablespoons water (allow both to sit for 10-15 minutes to thicken). I hope this helps!

    • Dr. Josh Axe on

      Hi Leah, you can substitute the maple syrup for honey, coconut nectar, dates or stevia. If you use stevia, make sure to greatly reduce the quantity. I would personally recommended trying honey or coconut nectar because they are most similar to maple syrup. I hope this helps!

    • Dr. Josh Axe on

      I am so glad to hear that you enjoyed the carrot cake! If you are referring to liquid bone broth, you can purchase or make vegetable broth. As a powder substitute, you can look for pea protein blends. I hope this helps!

  14. TJ on

    FYI Folks-These are delicious. I would recommend them to anyone. I admit I was skeptical but followed the recipe exactly. I did bake them in the mini muffin pan but still baked them the full time. Be aware that they aren’t going to ‘spring back’ when touched at the end of baking….you will think they aren’t cooked enough. I finally decided they just needed to cool to firm up and they did. I did not frost these….I don’t think they need frosting! They are yummy as is. Thanks for this recipe. Sometimes those of us who are recovering sweet tooths just want a healthier treat. I also like that I just throw the ingredients together with no monkey business. This is a winner.

  15. Seda on

    Hello! It looks great. Can we use only coconut flour? If yes, how much coconut flour in total we should add? Thanks a lot :)


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