These gluten-free carrot cake cupcakes bake up ultra-moist (thanks to loads of finely grated carrots), with a tender and fluffy crumb. They're incredibly flavorful thanks to warm spices and the sweet carrots. Studded with walnuts and topped with coconut cream cheese frosting, these are the best carrot cake cupcakes I've ever had!

Gluten-Free Carrot Cupcakes Top Down with Bite Close-up

You know what's better than a cupcake? A cupcake that's also delicious enough to be eaten as a muffin for days when you just can't be bothered to make frosting. These gluten-free carrot cake cupcakes are exactly that. Now, I'm not saying you should skip the frosting, I'm just saying you can.

The crumb is fluffy, tender, and ultra-moist, with spices, toasted walnuts, and loads of grated carrots. When coconut cream cheese frosting gets swirled on top, these become the world's best cupcakes.

I adapted these cupcakes from my gluten-free carrot cake recipe layered high with honey cream cheese frosting. When I tested the carrot cake directly as cupcakes, they baked up more dense than I wanted for a cupcake, so I tested and tweaked several times to create the perfect fail-proof carrot cake cupcake recipe.

Rather than chestnut flour, these carrot cake cupcakes use almond flour for the base, exchanging some of the butter for more milk to create a lighter, fluffier cupcake that's still just as moist. As a finishing touch, they're topped with swirls of coconut cream cheese frosting.

Why you'll fall head over heels for these carrot cake cupcakes

They’re versatile cupcake/muffin hybrids: When you're low on energy, this crumb is delicious enough to eat as a muffin. Aka breakfast is served. Frosting is optional (though highly encouraged).
Moist while still tender and fluffy: The texture hits that dreamy balance of tender and hearty.
That coconut cream cheese frosting though: It’s silky, tangy, and lightly tropical - flavors that pair beautifully with the spiced carrot cupcake crumb.

Plate of Gluten-Free Carrot Cake Cupcakes with Almond Flour

Important Ingredient Notes Before you Bake

Whole milk + vinegar: Mixing vinegar with whole milk is an easy buttermilk swap. For these cupcakes, I prefer milk + vinegar over buttermilk - it makes the cupcakes lighter, fluffier, and just as flavorful.
Granulated sugar + brown sugar: Granulated sugar keeps the texture light and fluffy - which is essential for cupcakes! - while brown sugar adds moisture and deep caramelly notes.
Unsalted butter + coconut oil: Butter adds rich flavor, while coconut oil keeps the cupcakes extra moist and tender. It’s a little baking magic trick that makes the crumb super soft without being greasy. I recommend refined coconut oil as it is more neutral with a less pronounced coconut flavor. You can also sub in plant butter for a dairy-free version.
Orange zest: Orange zest is like a secret flavor booster for carrot cake—it adds just the right amount of brightness, bringing out the natural sweetness of the carrots and balancing the warm spices with a subtle citrusy lift.
Shredded carrots: Finely grate your carrots using the fine grater on your box grater! I know it’s a bit of extra effort, but it makes a huge difference in the texture—super soft and evenly moist cupcakes without any stringy bites of carrot. Whatever you do: do not use pre-shredded carrots! You will be sad.
Chopped walnuts or pecans, toasted: Toasted nuts bring a nice crunch and a toasty, nutty flavor that cuts through the sweetness and makes each bite more interesting. Hot take: nuts just belong in carrot cake.

Ingredients for Gluten-Free Carrot Cupcakes

What I've Found to Be the Best Gluten-Free Flour Blend for Carrot Cupcakes

Super-fine blanched almond flour: When I tested the cupcakes with almond flour, I found that it highlights the subtle sweetness, adding rich nuttiness and plenty of moisture.
Gluten-free oat flour: Oat flour adds structure and softness for a fluffy, moist (but never dense) crumb. Oat flour's warm, wholesome flavor pairs perfectly with almond flour.
Sweet rice flour: The same flour used to make mochi, sweet rice flour is different from regular white rice flour. It’s gluten-free baking’s secret weapon, adding chewiness and helping hold everything together.

Coconut Cream Cheese Frosting

I've topped these carrot cupcakes with my quick and easy 5-minute coconut cream cheese frosting. It’s got a little extra butter, so it holds up perfectly for piping or swirling without getting soft or melty. The flavor stays true to classic cream cheese frosting but with a subtle tropical twist that takes things up a notch.

Prefer a more traditional version? Skip the coconut milk and swap the coconut extract for a splash more vanilla.

Overhead Gluten-Free Carrot Cake Cupcakes with Coconut Cream Cheese Frosting

How to Make Gluten-Free Carrot Cake Cupcakes

Here's how to make the fluffiest batch of 16 gluten-free carrot cupcakes:

Cream butter and sugars until pale and fluffy. Mix in the coconut oil, vanilla extract, and orange zest.

Mix in the eggs, one at a time.

Mixing in Finely Grated Carrots to Cake Batter

Mix in the finely grated carrots until evenly distributed and well combined.

Add the flour in two parts, alternating with the milk.

Folding in Walnuts to Gluten-Free Carrot Cupcakes

Fold in the toasted walnuts.

Unbaked Gluten-Free Carrot Cupcakes in Muffin Tin

Divide into prepared muffin tins, filling them ¾ full.

Note: This recipe has a lot of grated carrots and the batter may seem overly moist. If you notice the batter start to break with some moisture seeping out as it sits, don't fret! Just stir it before you put it into the muffin liners and I promise they'll bake up *chef's kiss*.

Baked unfrosted gluten-free carrot cupcakes on wire rack

Bake until the top springs back when gently touched. Let cool completely on a wire rack before slathering with this swoonworthy coconut cream cheese frosting.

Gluten-Free Carrot Cake Cupcakes with Bite Taken Out

Recipe