The best ever gluten free carrot cake muffins with a super simple and delicious cream cheese frosting! My favorite muffin recipe to date- these our out of this world good and you would NEVER know they are gluten free!!

This recipe is made in partnership with Bob’s Red Mill. I used their Super Final Almond Flour for these muffins, which is my favorite gluten free flour to bake with. It adds more protein, healthy fats, and fiber- such a great bonus. My favorite way to bake with their almond flour is mixing it with oat flour- the two combined add the best texture!

There is nothing better than a moist, flavorful, and perfectly sweet carrot cake muffin. One bite of these and you will be in absolute HEAVEN- I swear! I cannot get over how delicious these muffins turned out.

Can I make these dairy free?

Technically, yes. However, I don’t think any dairy free alternatives compare to the flavor of regular cream cheese! So, for the frosting I really recommend a real cream cheese!

Can I use a different flour for these muffins?

As I always say, baking is such a science. Using a different flour or changing the flours around will result in a completely different taste, texture, bake time, etc. These muffins will need to be kept as is with their ratios of almond flour, oat flour, and oats!

I am so excited to hear what you think of these Gluten Free Carrot Cake Muffins with the best ever cream cheese frosting! Enjoy! xo

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Gluten Free Carrot Cake Cupcakes with the Best Cream Cheese Frosting

  • Author: Mia Swinehart
  • Prep Time: 15 minutes
  • Cook Time: 17 minutes
  • Total Time: 32 minutes
  • Yield: 12 muffins 1x
  • Category: Dessert, Snacks


Moist and flavorful gluten free cupcakes with a simple cream cheese frosting!


  • 1/3 cup butter, melted (or sub coconut oil) ⠀
  • 2 large eggs ⠀
  • 1/3 cup maple syrup ⠀
  • 1/4 cup coconut sugar ⠀
  • 1/4 cup plain or vanilla greek yogurt (can sub dairy free yogurt or sour cream)
  • 1 tsp vanilla extract
  • 1 + 1/2 cups finely grated carrots (from ~2-3 carrots_
  • 1 + 1/3 cup Bob’s Red Mill Super Fine Almond Flour
  • 1/3 cup + 3 tbsp oat flour ⠀
  • 1/3 cup gluten free old-fashioned rolled oats
  • 1 + 1/2 tsp cinnamon
  • 1/2 tsp nutmeg ⠀
  • 3/4 tsp sea salt ⠀
  • 1 tsp baking soda ⠀
  • Optional add ins: raisins, pecans

For the Cream Cheese Frosting

  • 8 oz cream cheese, softened*
  • ¼ cup maple syrup
  • 1 tsp vanilla extract


  1. Preheat oven to 350°F and line 12 muffin tins with cupcake liners.
  2. In a large bowl, whisk the butter, eggs, maple syrup, coconut sugar, yogurt, and vanilla until smooth. Stir in the shredded carrots.
  3. Mix in the remaining dry ingredients, and stir until a smooth batter forms. If adding, fold in your pecans and/or raisins here.
  4. Scoop the batter into 12 muffin tins.
  5. Bake for 16-18 minutes, until a toothpick comes out mostly clean. Allow to cool.
  6. While muffins are cooling, use a hand mixer to beat the cream cheese until smooth, then add in the maple syrup and vanilla and mix until well-combined. Set in refrigerator until muffins are cool. Once muffins are frosted, store in the refrigerator for up to 6 days.


*While technically you can use dairy free cream cheese, for the best flavor results I really recommend a regular cream cheese here!

Breakfast, Dessert, Gluten Free, Recipes, Snacks, Vegetarian


Mar 10, 2022

Gluten Free Carrot Cake Cupcakes with the Best Cream Cheese Frosting

Did you make this recipe? Be sure to tag @gatherednutrition on INstagram so I can see what you made! Leaving a rating and review on the site is a huge help too!

  1. Bricelda Nunez says:

    This looks amazing!! Would I be able to use the exact measurements for a loaf tin instead of muffin tin?

    • Mia Swinehart says:

      I haven’t tried this in a loaf tin! I have a cake version of the blog if you search carrot cake! The bake time is different from the muffins so I recommend following that version!

  2. Katie says:

    These are so good! I didn’t have cream cheese so I omitted the cream cheese frosting and they were still amazing. Perfect for an Easter weekend breakfast!

  3. Helen says:

    This is a wonderful recipe – thank you!!! Hubby is T2D and so I used alullose sweetener mixed with some Golden Lakanto and it worked great. Cupcakes are moist and tender. Making more today.

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Simple. Attainable. Gathered Nutrition.