Healthy Low Sugar Carrot Cake Recipe with Greek Yogurt Cream Cheese Frosting – Gluten Free!

Celebrate anything with this low sugar carrot cake recipe! It is easy to make, perfect to share and has the most delicious greek yogurt cream cheese frosting. If you’ve been looking for a gluten-free and grain-free, healthy carrot cake recipe, this is it!

Healthy low sugar carrot cake recipe

Carrot cake is one of my favorites and instead of making a classic carrot cake, we’re mixing mixed it up making it gluten free, grain free, and made with way less sugar! It makes such a delicious cake that all carrot cake lovers will love! It is moist and made with wholesome ingredients.

I’ve also been making raisin carrot pancake muffins a lot lately (I need to share that with you too!), so I created this cake recipe based around that.

For the frosting, I kept it super simple and healthier than traditional cream cheese frosting. It is made with cream cheese, plain greek yogurt, maple syrup, and vanilla extract.

You’ll love the slight tang you get from the greek yogurt along with the cream cheese flavor that pairs beautifully with the cake.

If you’re looking for a different variation on a traditional carrot cake, be sure to also check out these carrot cake donuts! They can be turned into cupcakes or cake form just by adjusting the bake time. This baked cake recipe gives you a slightly denser cake. I loved the outcome and whether you’re looking for a gluten-free cake or not, it’s super delicious!

We don’t follow a gluten-free diet, but I find I often make foods naturally gluten-free and don’t try to overload our plates with one specific grain (ie – not always using wheat flour). I’d call us – gluten lite.

This carrot cake recipe uses a mixture of almond flour, tapioca flour, and coconut flour (which is based on my favorite pancake mix I’ve been making lately), and even had hidden pumpkin in the recipe! You could sub in applesauce for the pumpkin too.

Whatever you are celebrating, make this carrot cake part of the occasion! Bonus – no major sugar crash at the end of the night!

What you need for carrot cake with greek yogurt cream cheese frosting

Scroll down to view the recipe card below for the full ingredients list, nutrition facts, and step-by-step instructions.

• butter
• natural cane sugar
• pure maple syrup
• pumpkin puree
• eggs
• plain unsweetened almond milk
• vanilla extract
• almond flour
• tapioca flour
• coconut flour
• baking powder
• baking soda
• cinnamon
• sea salt
• grated carrot
• cream cheese
• plain greek yogurt
• pure maple syrup
• vanilla extract

How to make the best healthy carrot cake

1. Preheat the oven to 350 degrees F. Cover the bottom of 2 – 6″ cake pans with parchment paper then oil the sides and parchment paper.
2. In a large bowl, whisk the butter and sugar together. Add the maple syrup, pumpkin purée, eggs, almond milk, and vanilla extract, and fully mix the wet ingredients together.
3. In the same large mixing bowl, add the almond flour, tapioca flour, coconut flour, baking powder, baking soda, cinnamon, and sea salt, then stir the dry ingredients all together. Once the wet and dry ingredients are almost fully mixed, add in the grated carrots. For best results, stir just until there are no clumps and all the flour is mixed in.
4. Pour the cake batter into the prepared pans. Bake in a preheated oven for 45-50 minutes. Check for doneness by inserting a toothpick into the center of the cake. If it comes out wet, keep baking until only a dry crumb comes out on the toothpick.
5. Once the cakes are done baking and out of the oven, wait 10 minutes and flip the cakes into a cooling rack to fully cool.
6. When the cakes are fully cooled to room temperature, prepare the frosting by whisking together the cream cheese, greek yogurt, maple syrup, and vanilla extract. If your yogurt gives you some clumps, just keep whisking, they will eventually smooth out. You can also whisk in a stand mixer.
7. Assemble the cake by placing one cooled cake on a cake stand. Add a thin layer of frosting on top. Add the second cooled cake. Thinly frost the sides. Add the remaining frosting to the top of the cake!
8. To decorate, make a carrot rose by peeling the length of a full carrot and then spiraling it into a circle. Add chopped pistachios for pretty color on top! Shredded coconut flakes are another fun option to top your cake with.

Best-size cake pans

These 6″ cake pans are perfect for smaller cakes! I used 2 in this recipe. Here is the cake stand I use!

You can also bake this cake in a 9″ X 13″ pan. Increase the bake time for the larger size.

Can you make these cupcakes?

Absolutely! Turn your homemade carrot cakes into healthy carrot cake cupcakes! Start by making the recipe and baking as you would for carrot cake muffins in a muffin tin. The baking time will decrease to closer to 18-24 minutes.

While the cupcakes bake you’ll make the luscious cream cheese frosting. Frost the cooled cupcakes and enjoy!

Prep in advance

To make this cake recipe in advance, fully bake the cake and allow it to cool. You can make this up to 5 days in advance, and then wrap it tightly in plastic wrap to store in the fridge.

The frosting can be made in advance as well and stored in the fridge in an airtight container.

Frost the cakes the day of and enjoy!

Substitutions

Below you’ll find a list of substitutions that will work well in this gluten-free carrot cake recipe. 

If you try something different out, please leave a comment below letting us all know how it turned out!

Butter – Instead of butter, coconut oil, ghee (which is clarified butter), or even light olive oil can be used here.

Natural cane sugar – Coconut sugar, white sugar, brown sugar, or your go-to granulated sugar will all work here. The flavor profile will change slightly when using coconut sugar or brown sugar, but it works well in this low sugar carrot cake recipe!

Maple syrup – Honey and agave nectar will work as liquid sweeteners to use in place of the maple syrup. Honey browns a little faster in baked goods compared to maple syrup, so keep your eye on how quickly the cake is browning and cover if needed.

Pumpkin puree – Applesauce is a great alternative to use here.

Almond milk – Use any type of milk here. Keep it dairy free with coconut milk, hemp milk, or oat milk, or use regular milk in place of almond milk.

Almond flour – Almond meal will work in place of the super fine almond flour. It will result in a less smooth cake, but the flavor will be delicious! If you don’t need to keep this recipe gluten-free, use regular whole wheat flour or white whole wheat flour can be used in place of almond flour too.

Tapioca flour – Tapioca flour can be substituted equally with tapioca starch, arrowroot powder, or cassava flour.

Coconut flour – To omit the coconut flour, use almond flour instead but double the amount since coconut flour absorbs more liquid than other flours.

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If you try this best carrot cake recipe, I’d love it if you left a star rating and comment below letting me know how it turned out!

XO

Heather

*Originally published November 2018. Updated March 2023.*