Paleo Carrot Cake Cupcakes (Healthier, Gluten Free)

These paleo carrot cake cupcakes are so perfect: moist, tender, and flavorful. On top of that, they’re super easy and quick to pull together. Perfect for Easter or just for a healthier snack or dessert. Gluten free, grain free, and dairy free option.

Let’s put carrots in cake, they said! It’ll be delicious, they said! And, well, as much as I hate admitting when other people are right, they were really right.

And these paleo carrot cupcakes are especially right. In fact, you’d never know they’re gluten free, healthier, paleo, and refined sugar free (with a dairy free option!). You just wouldn’t! They’re moist and perfectly spiced and tender and ugh ugh ugh, I could eat them all the time. And have eaten them for breakfast. You see, they have a vegetable and also a fruit and some nuts and eggs, too, so what part of that doesn’t sound like breakfast to you? Challenge me!

What Makes This Recipe So Good

These carrot cake cupcakes are paleo, gluten free, grain free, and dairy free, too! But here’s a fun dose of trickery: you would seriously never know they’re grain-free. Try it as a parlor game with your friends! See who says, “Weird, is there, like, no all-purpose flour in here or something? I don’t quite taste the super refined sugar, either.” Literally no one will say that. Literally zero people. In fact, they’ll all be like, “That’s so weird, because I could’ve sworn you said you’d gone paleo.”

Joke’s on you, suckers! Just kidding. Joke’s on no one, because we all win with these fab paleo carrot cake cupcakes.

There’s a regular ol’ dairy cream cheese frosting option that I highly recommend, if you’re into that kind of thing. Oh, and they’re damn delicious without the frosting, too, so you can leave that swipe of tangy, creamy deliciousness off entirely and call it a [paleo carrot cake muffin] day.

But like, why would you ever opt out of frosting? Just saying.

Why You’ll Love This Recipe

• They’re moist and tender, and they’re loaded with flavor.
• This paleo carrot cake has pineapple, pecans, cinnamon, ginger, and, of course, carrots. All the classic ingredients for a carrot cake in a little paleo package!
• These paleo carrot cake cupcakes are also gluten free, grain free, refined sugar free, and dairy free (as long as you use dairy-free cream cheese, of course!).
• This recipe is crazy easy to make, and it comes together very quickly!

How to Make Them

Start by grating your carrots. I prefer to to do this in a food process with the grating attachment attached; it goes super quickly and I don’t grate the skin off any of my fingers. You can, however, go about this the old-fashioned way: grate carrots on a box or hand grater until you produce 1 1/2 cups. That’s about 3 medium carrots.

Next, whisk your eggs in a large bowl, then add in your sugar, melted coconut oil, and vanilla extract. Whisk well, then stir in the drained crushed pineapple and your dry ingredients. That means the almond flour, coconut flour, tapioca flour, baking soda, salt, cinnamon, and ginger. Whisk well until flours are all incorporated, then fold in the chopped pecans.

Line 12 muffin tins with paper liners, preferably parchment paper liners. Fill the liners completely full, then bake in a 350º F oven for 20-25 minutes or until a toothpick inserted in the middle comes out clean. Remove from oven and let cool slightly, then remove cupcakes and cool completely on a wire rack.

Meanwhile, make your cream cheese frosting. Add softened cream cheese (dairy-free or conventional) to a medium bowl, along with maple syrup, softened coconut oil, and vanilla extract. Using a handheld mixer, beat on high until completely smooth.

Set the frosting aside until cupcakes are completely cooled, then frost. Garnish with a sprinkle of chopped pecans, if desired.

Cream Cheese vs. Dairy-Free Cream Cheese Frosting

If you’re avoiding all dairy, definitely go with the dairy-free cream cheese frosting option. I personally like Kite Hill and Miyoko’s the best and find them to be the closest to the real thing. The texture won’t be quite as thick as traditional cream cheese. However, it’ll make the entire recipe dairy free, so that’s a big win!

I recommend using regular, organic cream cheese, as it’s tangier, thicker, and richer than dairy-free cream cheese. If you typically avoid dairy, you may want to consider cultured cream cheese, as this, like yogurt, will be easier on your digestion than conventional cream cheese. Nancy’s is a great brand to try!

Baking Tips

Use parchment paper liners for the easiest ever muffins and cupcakes. I actually have trouble with these sticking to the cooled carrot cake cupcakes at all, they’re that nonstick!

Test the cupcakes with a toothpick after 20 minutes. You’ll see a couple crumbs but the toothpick will otherwise be clean. Test early so as not to overbake.

Bake the paleo carrot cake cupcakes in the middle rack of your oven where the heat is most even. I have not tested this recipe using convection.

Other Recipes You’ll Love

• Best Chocolate Paleo Cupcakes Ever with Dark Chocolate Frosting
• Peach Ginger Paleo Muffins
• Carrot Cake Paleo Breakfast Bake with “Cream Cheese” Glaze
• Paleo Pumpkin Chocolate Chip Muffins with Cream Cheese Frosting (Dairy-Free, GF)

Hey – you’ve made it this far, so now we’re basically best friends! If you make this recipe, I’d love for you to give it a quick review & star rating ★ below. Make sure you follow me on Instagram, Pinterest, TikTok, and Facebook, too!

4.89 from 67 votes

Paleo Carrot Cake Cupcakes with Cream Cheese Frosting

Prep:10 minutes

Cook:20 minutes

Cooling Time:30 minutes

Total:30 minutes

Moist gluten free carrot cake cupcakes topped with creamy, tangy cream cheese frosting. Packed with pineapple, pecans, spices, and carrots, like a traditional carrot cake, but gluten free, grain free, refined sugar free, and with a dairy free option.

• Pin

Print Save Saved! Go Premium - Ad Free + Meal Plans!

12 cupcakes

Ingredients

• ▢ 2 large eggs
• ▢ 1/2 cup coconut sugar
• ▢ 1/3 cup refined coconut oil melted
• ▢ 2 teaspoons vanilla extract
• ▢ 1 8- oz. can crushed pineapple in juice drained, about 1 cup
• ▢ 1 1/2 cup grated carrots
• ▢ 1 1/2 cups almond flour
• ▢ 2 tablespoon coconut flour
• ▢ 2 tablespoon tapioca flour
• ▢ 1 teaspoon baking soda
• ▢ pinch salt
• ▢ 1/2 teaspoon cinnamon
• ▢ 1/4 teaspoon ground ginger
• ▢ 1/2 cup chopped pecans

Cream Cheese Frosting

• ▢ 8 ounces cream cheese or dairy-free cream cheese softened, see Note 1
• ▢ 1/4 cup pure maple syrup
• ▢ 1/4 cup refined coconut oil softened
• ▢ 1/2 teaspoon vanilla extract
• ▢ pinch ground ginger

Instructions 

• Preheat oven to 350º F. Line a muffin tin with 12 paper liners, preferably parchment paper liners.
• In a large bowl, whisk eggs. Stir in coconut sugar, melted coconut oil, and vanilla extract. Stir together until well combined. Add in drained crushed pineapple, carrots, and dry ingredients: almond flour, coconut flour, tapioca flour, baking soda, salt, cinnamon, and ginger. Whisk well until well combined and smooth, then fold in chopped pecans.
• Portion out batter into lined cupcake tin, filling each completely full. Recipe will make approximately 11-12 cupcakes. Bake on the middle rack for 20-25 minutes or until a toothpick inserted into the middle comes out clean. Remove from the oven and let cool for a few minutes, then remove cupcakes from the tin and let fully cool on a wire rack.
• In the meantime, make your cream cheese frosting. Combine softened cream cheese, maple syrup, softened coconut oil, vanilla extract, and ground ginger in a medium bowl. Beat with a stand or handheld mixer until completely smooth. Set aside.
• When cupcakes are completely cool, frost with an offset spatula or butter knife. You can also pipe a swirl onto the top of the cupcake then smooth with a spatula or butter knife. Garnish with a sprinkle of finely chopped pecans, if desired.

Notes

Note 1
For dairy-free cream cheese, I like Kite Hill and Miyoko's. If you are paleo but eat some dairy, try a cultured dairy cream cheese like Nancy's! I definitely recommend the dairy version of this frosting if you tolerate it.

Note 2
To test cupcakes for doneness, insert a toothpick into the center of a cupcake. The toothpick should come out clean with a few crumbs.

Note 3
I love parchment paper cupcake liners because they're so reliably nonstick. In fact, they're so nonstick that they have a little trouble staying on these muffins. If you're displaying or transporting these, you might want to use regular paper muffin liners here.

Note 4
For the frosting, make sure the coconut oil is quite soft. Otherwise, you will have a lumpy frosting full of little beads of solidified coconut oil. Using melted to make the frosting is OK, so long as you give the frosting plenty of time to solidify before frosting.

Video

Nutrition Information

Calories: 296kcal, Carbohydrates: 21g, Protein: 5g, Fat: 22g, Saturated Fat: 8g, Cholesterol: 48mg, Sodium: 189mg, Potassium: 147mg, Fiber: 3g, Sugar: 13g, Vitamin A: 2975IU, Vitamin C: 3mg, Calcium: 71mg, Iron: 1mg, Net Carbs: 18g

Number of total servings shown is approximate. Actual number of servings will depend on your preferred portion sizes.

 

Nutritional values shown are general guidelines and reflect information for 1 serving using the ingredients listed, not including any optional ingredients. Actual macros may vary slightly depending on specific brands and types of ingredients used.

 

To determine the weight of one serving, prepare the recipe as instructed. Weigh the finished recipe, then divide the weight of the finished recipe (not including the weight of the container the food is in) by the desired number of servings. Result will be the weight of one serving.