Gluten Free Carrot Cake Cupcakes are an easy, allergy-friendly, and tasty take on a classic springtime treat. These moist cupcakes are packed with carrots, juicy pineapple, almonds, and cranberries and can be made in a single bowl in under 1 hour! 

Celebrate the spring flowers and warm summer weather with moist and flavorful fruit-based desserts. My Gluten-Free Lemon Cupcake, Peach Cobbler with Biscuits, Lemon Blueberry Buttermilk Cake, and these Gluten Free Carrot Cake Cupcakes are deliciously wonderful ways to use up leftover produce and celebrate the season. Plus, as far as desserts go, these cupcakes are about as healthy as it gets!

Gluten Free Carrot Cake Cupcake with cream cheese frosting. A mini carrot on top.

These moist and sweet carrot cake cupcakes are an absolute superstar of a dessert. Not only are they gluten and dairy free, but they’re also free from refined sugars and can easily be made nut free. While they’re an especially perfect dessert for Easter and a Mother’s Day brunch, you can pack up the batch and bring them anywhere, anytime. Everyone is sure to love them!

The process is easy: make the batter in one bowl, bake, then top with a generous swirl of cream cheese frosting. You can even prep them ahead of time or really wow your guests by baking this simple cupcake batter into a full-sized carrot cake!

Gluten Free Carrot Cake Cupcake with cream cheese frosting. A mini carrot on top.

Ingredient notes

  • Gluten free flour – Any 1:1 gluten free flour blend will work beautifully. I would avoid using single-source gluten free flours such as coconut or almond flour because they don’t absorb moisture quite as well. If you don’t need the recipe to be gluten free, go ahead and use whole wheat or all purpose flour.
  • Carrots – Because what’s a carrot cake dessert without some finely shredded carrots?
  • Crushed pineapple – Canned or fresh will give these cupcakes lots of moisture and a sweet and acidic tang.
  • Olive oil – This acts as the main source of moisture in the cake. Coconut oil or avocado oil work just as well. To make oil free cupcakes, replace the oil with applesauce.
  • Maple syrup – This natural sweetener adds a nice sugary warmth. Agave syrup, liquid stevia extract, or honey can also be used.
  • Slivered almonds – These nuts are completely optional, but add just the right amount of crunch. Feel free to use walnuts, pistachios, pumpkin seeds, or hazelnuts instead.
  • Cranberries – Roasted or dried cranberries will work here.
  • Cream cheese frosting – While this frosting isn’t dairy or refined sugar free, it is the perfect finishing touch on top. You can always leave it off or replace it with a dairy free alternative.
Gluten-free carrot cake cupcakes on a tray with cream cheese frosting. A mini carrot on top.

How to make gluten free carrot cake cupcakes

This easy one-bowl carrot cake cupcake recipe is an exciting twist on a classic spring dessert. You can whip up a batch of these sweet little cakes in just six simple steps:

Step 1: Add the eggs, shredded carrots, crushed pineapple, olive oil, vanilla extract, and maple syrup to a stand mixer. Whisk until thoroughly combined. 

Step 2: Slowly add the flour, baking powder, cinnamon, and salt. Mix until just combined.

Step 3: Use a rubber spatula to gently fold in the cranberries and almonds. 

Step 4: Pour the batter into a lined cupcake tin and bake until golden brown. Remove the cupcakes from the oven and let them cool.

Step 5: While the cupcakes are baking, make the cream cheese frosting by beating together the cream cheese, powdered sugar, and vanilla extract until smooth.

Step 6: Transfer the icing to a piping bag and pipe a generous amount of cream cheese frosting on top of each carrot cake cupcake. Decorate with additional carrots if desired, then serve and enjoy!

Gluten-free carrot cake cupcakes on a tray with cream cheese frosting. A mini carrot on top.

Make a full-sized cake instead

This recipe makes enough batter to fill one well-greased 9-inch round cake pan. The recipe can also be doubled or tripled to make 2-layer or 3-layer cakes instead. Bake the carrot cakes in a 350ºF oven for 35 to 45 minutes.

Storing and freezing

To store: Place any leftover gluten free carrot cake cupcakes into an airtight container and store them on the counter for up to 3 days or in the fridge for up to 1 week.

To freeze: Wrap your unfrosted carrot cake cupcakes in plastic wrap and store them in the freezer for up to 3 months. Let them thaw before frosting them with a fresh batch of cream cheese icing.

carrot cake cupcake taken a bite off.

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carrot cake cupcake gluten-free
5 from 4 votes

Gluten Free Carrot Cake Cupcakes

by Silvia Dunnirvine
Gluten Free Carrot Cake Cupcakes are an easy and tasty take on a classic springtime treat. They’re made in a single bowl in under 1 hour!
Prep: 22 minutes
Cook: 25 minutes
cooling time: 5 minutes
Total: 47 minutes
Servings: 9 jumbo cupcakes


  • 2 large cage-free eggs
  • 2 cups shredded carrots
  • 1 1/2 cups crushed pineapple, fresh or canned
  • 1/4 cup olive oil
  • 1/2 tbsp vanilla extract
  • 1/3 cup maple syrup
  • 2 cups 1-to-1 gluten free flour
  • 1 tbsp baking powder
  • 1/2 tsp cinnamon
  • 1 pinch sea salt
  • 1 cup shaved/ slivered/ crushed almonds
  • 1 cup baking cranberries

Cream Cheese Frosting

  • 8 oz cream cheese
  • 1 tsp vanilla extract
  • 1/2 cup powdered sugar


  • Turn oven on 375F degrees. Line muffin pan with liners, muffin molds or silicone mold and set aside. 
  • Add the first six ingredients to a stand mixer, one at a time and mix using the whisk attachment on medium speed until well incorporated. 
  • Switch to the paddle attachment. Add the flour, one cup at a time. Followed by baking powder, cinnamon and salt. Mix until well combined. Turn off mixer and remove bowl from stand. Fold in almonds and cranberries.
  • Scoop the dough into the muffin cups about 3/4 full. Bake for 23-25 minutes. Tops should be golden brown. Insert a toothpick to make sure it’s fully cooked inside (toothpick should come out clean). See notes* Remove from oven allow it to cool down.

Cream Cheese Frosting

  • Add cream cheese, powdered sugar and vanilla extract to a bowl and mix using a hand mixer or you can use the stand mixer, until smooth and well incorporated. 
  • When cupcakes are cooled down, spread a generous layer of cream cheese on top using a piping bag or spatula.

Carrot Topping

  • Cut 1 1/2 – 2 inches of the end of a carrot then slice it in half lengthwise. Place one half cut side down on top of the cream cheese frosting and place a few rosemary leaves on top. 


*Recipe times for 9 jumbo muffins, if you are making smaller muffins cook for 18-21 minutes. 


Calories: 467kcal | Carbohydrates: 61g | Protein: 9g | Fat: 22g | Saturated Fat: 7g | Polyunsaturated Fat: 3g | Monounsaturated Fat: 11g | Trans Fat: 1g | Cholesterol: 67mg | Sodium: 263mg | Potassium: 342mg | Fiber: 4g | Sugar: 32g | Vitamin A: 5171IU | Vitamin C: 5mg | Calcium: 177mg | Iron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Keyword: Cupcake, Easter
Course: Breakfast, Dessert
Cuisine: American
Like this? Leave a comment below!

Hi! I’m Silvia.

My goal is to make cooking simple and enjoyable.

Garden in the Kitchen is full of easy and balanced recipes for busy families. Classics get a healthier twist with additions of veggies or alternative ingredients.

I hope my recipes will inspire you to cook more home meals and above all have fun in the kitchen!

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Recipe Rating


  1. Those cupcakes look sooo GOOD! Have fun with them. hehe 🙂

    No idea what a saltena is, but that looks delish, too!

  2. I made this on the stove top with slightly less sugar and I was amazed at how delicious this recipe was. Will definitely be making again and again. Thank you!