
This easy and delicious carrot cake cupcakes recipe is served with our yummy cream cheese frosting. You’ll fool everyone with these! It’s our favorite healthier cupcake recipe and we’ve made it countless times over the last few years, tweaking and perfecting with every batch.

How To Make Healthy Carrot Cake Cupcakes From Scratch:
This easy recipe is crazy quick to throw together and believe me, it’s incredibly hard to believe you’re eating a healthier carrot cake cupcake.
Made with almond flour and other healthy ingredients, these little cupcakes contain a lot of nutritional goodness. Isn’t is just amazing how making smart ingredient swaps can take something from “empty calories” to being filled with nutrients.
Almond flour by itself is PACKED with nutrients*, and when you add carrots, pecan nuts, eggs and spices - you’re just adding to the goodness.
*(See THIS great article from healthline.com about why almond flour is healthier than most other flours.)
It’s gluten-free and paleo approved, and can be low-carb keto friendly if you use a honey substitute. (We like THIS one).
The Ingredients You Need:
You need just 7 simple ingredients (and a few spices) to make these to-die for carrot cake cupcakes:
- Almond Flour
- Baking Powder
- Cinnamon, Ginger, Nutmeg
- Eggs
- Coconut Oil
- Honey (Use THIS honey substitute for a low-carb and keto approved version)
- Shredded Carrots
- Chopped Pecan Nuts
Step-By-Step Instructions:

- Add all the ingredients (except the carrots and pecan nuts) and use a whisk to mix until smooth and lump-free.
- Now, add the shredded carrot and roughly chopped pecan nuts.
- Stir until everything is evenly distributed through the batter.
- Now, divide the batter between 8 cupcake liners. (This will be affected by the size of the muffin tin), but generally we get 8-9 cupcakes per batch.
- Now bake at 180C/350F for approximately 20 minutes. The cupcakes are done when a toothpick pressed into the middle of the cupcake comes out clean.
- Remove the cupcakes from the pan, and allow to cool on a wire rack.
- Once cooled, frost with our super simple and delicious Cream Cheese Frosting. This really bring out the best in carrot cake cupcakes.
Looking For More Healthier Cupcake Recipes?
For more healthy low carb keto and paleo cupcake recipes, check out our uber delicious basic Vanilla Coconut Flour Muffin and our super delicious Paleo Blueberry Muffins. We also have some of our personal favorite healthy muffin recipes from other great bloggers rounded up here: Healthy Paleo Muffin Recipes.
Did You Make This Recipe?

If you’ve made our Gluten-Free Carrot Cake Cupcakes recipe, please leave a comment and a rating. We love hearing your feedback and it greatly helps us improve our recipes!
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📋 recipe

Gluten-Free Carrot Cake Cupcakes
Ingredients
Dry Ingredients:
- 1 ¼ cup almond flour
- 1 teaspoon baking powder
- 1 teaspoon ground cinnamon
- ½ teaspoon ground ginger
- ¼ teaspoon nutmeg
- ⅓ cup pecan nuts (roughly chopped)
Wet Ingredients:
- ⅓ cup coconut oil
- ⅓ cup honey
- 2 teaspoon vanilla essence
- 1 cup shredded carrots
Instructions
- Preheat your oven to 180C/350F
- Add everything (except the carrot and pecan nuts) into a large mixing bowl.
- Whisk together until smooth and lump-free.
- Add the carrot and pecan nuts.
- Stir until evenly distributed.
- Divide between 8 lined muffin tin cups.
- Bake for approximately 20 minutes.
- Allow to cool completely on a wire rack before frosting.
Tips and Tricks:
- The cupcakes are done when a toothpick pressed into the center of the cupcake comes out clean.
- We use our Cream Cheese FrostingCream Cheese Frosting to really bring out the best in these carrot cake cupcakes.
- Save a little bit of the chopped pecan nuts to sprinkle on top as a beautiful garnish.
Miguel says
Eggs.