Gluten-Free Carrot Cake Muffins and Cream Cheese Glaze

This is the best-tasting Gluten-Free Carrot Cake Muffins and Cream Cheese Glaze Recipe for a delicious breakfast or snack. These healthy muffins are made with almond flour, oat flour, and cassava flour and naturally sweetened with cane sugar, raisins, applesauce, and cottage cheese and topped with cinnamon, toasted coconut, and chopped pecans.

ByNicole Bonilla
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Gluten-free carrot cake muffins with cream cheese glaze on a kitchen counter.

This is the best-tasting Gluten-Free Carrot Cake Muffins and Cream Cheese Glaze Recipe for a delicious breakfast or snack. These healthy muffins are packed with the goodness of grated carrots and topped with a luscious cream cheese frosting. They’re gluten-free with almond flour, oat flour, and cassava flour and naturally sweetened with cane sugar, raisins, applesauce, and cottage cheese. The cream cheese glaze adds a little sweetness and is topped with cinnamon, toasted coconut, and chopped pecans.

These gluten-free carrot cake muffins are perfect for busy mornings or a healthier dessert for Thanksgiving, Easter, or anytime you have a sweet carrot craving. With the best texture you’ll find in a carrot cake muffins recipe, they’re sure to become your new favorite carrot cake treat.

YouTube video

Why You’ll Love This Healthy Carrot Cream Cheese Muffin Recipe

  • You only need a few simple ingredients.
  • It is super easy to make for an impressive result.
  • The flavor-rich ingredients make it taste amazing!
  • All the ingredients are easily digestible for a gentle tummy.
Gluten-free carrot cake muffins with cream cheese glaze on a kitchen counter.

Ingredients & Substitutions

Here is everything you need to make the best-tasting carrot cake muffin recipe:

Eggs: Feel free to use any variety of eggs you like. Flax eggs (3 tablespoons ground flaxseed mixed with 9 tablespoons water) or chia eggs (3 tablespoons chia seeds mixed with 9 tablespoons water) can also be used in the same amount.

Cane Sugar: Any type of granular sugar will work. You can also use maple syrup, honey, or a natural sweetener like stevia or monk fruit, adjusting the amount based on sweetness.

Cottage Cheese: You can opt for any variety of cottage cheese. Greek yogurt, ricotta cheese, or dairy-free yogurt can also be used as substitutes in the same amount.

Unsweetened Applesauce: Use any type of applesauce you prefer. Mashed bananas or pumpkin puree are good alternatives in the same amount.

Avocado Oil: Any variety of avocado oil is suitable. You can also substitute with coconut oil, melted butter, or any neutral oil like grapeseed oil in the same amount.

Almond Flour: This is different than almond meal. You can replace it with an equal 3/4 cup of oat flour.

Oat Flour: Feel free to use any variety of oat flour. Brown rice flour can be used instead in the same amount. You can make your own oat flour by blending old-fashioned rolled oats or quick oats in a blender.

Cassava Flour: This helps the muffins bake light and improves elasticity. You can replace it with a gluten-free flour blend in the same amount. Or you can replace it with 1/2 cup of tapioca flour and increase the oat flour to 1-1/4 cups. 

Golden Raisins: You can use any variety of raisins. Regular raisins, dried cranberries, or chopped dried apricots are suitable alternatives in the same amount.

Shredded Carrots: Any type of shredded carrots can be used. Zucchini (squeezed to remove excess moisture), sweet potato, or parsnips are good substitutes in the same amount.

Shredded Coconut: Feel free to use any variety of shredded coconut. Chopped nuts like pecans or walnuts, or additional shredded carrots can also be used in the same amount.

Cinnamon, Dried Ginger and Nutmeg: You can omit any of these or replace them with an equal amount of pumpkin pie spice to maintain the fall taste of these muffins.

Cream Cheese Glaze

Powdered Cane Sugar: Use any type of powdered cane sugar you like. Powdered coconut sugar, a blend of powdered erythritol and stevia, or any powdered sugar alternative can also be used in the same amount.

Cream Cheese: Any variety of cream cheese will work. Dairy-free cream cheese or a blend of Greek yogurt and a small amount of coconut oil can be used as substitutes in the same amount.

Butter: Feel free to use any type of butter. Coconut oil, dairy-free butter, or ghee can also be used in the same amount.

Almond Milk: Any variety of almond milk is suitable. Plant-based milks like oat, soy, or coconut milk, or regular dairy milk can also be used in the same amount.

Lemon Juice: Use any type of lemon juice you prefer. Apple cider vinegar, lime juice, or a small amount of white vinegar are suitable alternatives in the same amount.

Gluten-free carrot cake muffins with cream cheese glaze on a kitchen counter.

How to Make My Cream Cheese Glazed Carrot Muffin Recipe

Here are easy, detailed, step-by-step instructions for making this healthy carrot muffin recipe. The instructions are also repeated in the recipe card at the bottom of this blog post.

Step 1: Make the Muffin Batter

Preheat your oven to 425°F and line a muffin tin with paper liners or lightly grease it. Blend the cottage cheese smooth in a food processor, upright blender or chopper cup of an immersion blender to remove the curdled texture.

In a large mixing bowl, whisk together the eggs, cane sugar, cottage cheese, unsweetened applesauce, avocado oil, vanilla extract, and apple cider vinegar until well combined.

Add the dry ingredients, including almond flour, oat flour, cassava flour, baking powder, baking soda, cinnamon, salt, ginger, and nutmeg. Whisk until just combined.

Gently fold in the golden raisins, shredded carrots (3 medium-sized carrots), and shredded coconut with a spatula until combined.

Combining wet ingredients to muffin batter.
Adding dry ingredients to muffin batter.

Step 2: Bake the Muffins

Divide the batter evenly among the muffin cups, filling each almost full. Allow the batter to mound higher in the middle for a higher dome.

BAKING OPTION 1:

To achieve a higher dome on the muffins, bake at 425°F for 5 minutes. Then, leave the muffin tin in the oven, reduce the heat to 350°F, and bake for 20-22 minutes, or until golden brown and a toothpick inserted into the center of a muffin comes out clean. 

BAKING OPTION 2:

Bake 350°F for 25-28 minutes, until golden brown and a toothpick inserted into the center of a muffin comes out clean.

Allow the muffins to cool in the tin for 5 minutes, then transfer them to a wire rack to cool completely.

Scooping muffin batter into muffin pan.

Step 3: Glaze the Muffins

In a small bowl, beat together the powdered cane sugar, room temperature cream cheese, butter, vanilla extract, almond milk, and lemon juice until smooth and creamy.

Once the muffins are completely cool, drizzle the cream cheese glaze over the top of each muffin.

Optional: sprinkle a hint of cinnamon, toasted coconut and chopped walnuts or pecans on top of the muffins. Allow the glaze to cool and set and enjoy!

Adding powdered sugar to cream cheese glaze.
Gluten-free carrot cake muffins with cream cheese glaze on a kitchen counter.

Helpful Recipe Notes

Baking Time: Baking the muffins at a higher temperature and then reducing it will give a heat boost to the muffins, resulting in a higher dome.

Spice Flavor: Adjust the amount of spices to your taste. For an extra flavor kick, add a pinch of cloves or cardamom.

Glaze Consistency: If the glaze is too thick, add more almond milk a teaspoon at a time until it reaches the desired consistency. If it’s too thin, add a bit more powdered sugar.

Toasted Coconut: Adding toasted coconut on top of the muffins is optional but adds flavor and texture! Bring a frying pan to medium heat and melt 1 teaspoon of butter. Add 1/3 cup of coconut and several pinches of salt. Continuously stir the coconut for several minutes until it is lightly toasted.

Store the glazed muffins in an airtight container in the refrigerator for up to a week. For longer storage, freeze the muffins (without glaze) in a sealed container for up to 3 months. Thaw and glaze before serving. The glaze can be stored separately in the fridge for up to a week.

Can I make this gluten-free recipe dairy-free?
Yes, you can substitute the cottage cheese with dairy-free yogurt, and use dairy-free cream cheese and butter in the glaze.

What can I use instead of eggs?
You can use flax eggs (3 tablespoons ground flaxseed mixed with 9 tablespoons water) or chia eggs (3 tablespoons chia seeds mixed with 9 tablespoons water).

Can I use different flours if I don’t have almond, oat, or cassava flour?
Yes, you can substitute almond flour with sunflower seed flour or a gluten-free all-purpose flour blend, oat flour with quinoa, sorghum, or millet flour, and cassava flour with tapioca or arrowroot flour, though the texture may vary.

What can I use instead of cane sugar in gluten free carrot muffins?
You can use coconut sugar, maple syrup, honey, or a natural sweetener like stevia or monk fruit, adjusting the amount to taste.

How can I make the glaze thicker or thinner?
To thicken the glaze, add more powdered sugar. To thin it, add more almond milk (or any milk) a teaspoon at a time until you reach the desired consistency.

Can I use different add-ins like nuts or other dried fruits in carrot gluten-free muffins?
Yes, feel free to substitute golden raisins with regular raisins, dried cranberries, or chopped dried apricots. You can also add chopped nuts like pecans or walnuts instead of shredded coconut.

What can I use instead of shredded carrots in healthy carrot cake muffins?
You can use shredded zucchini (make sure to squeeze out excess moisture), sweet potato, or parsnips.

How can I make this recipe as vegan carrot cake muffins?
To make these carrot cake muffins vegan, replace the eggs with flax or chia eggs, use dairy-free yogurt or vegan sour cream instead of cottage cheese, ensure cane sugar is vegan, and substitute dairy ingredients like cream cheese, butter, and milk with their plant-based counterparts. These adjustments will give you delicious vegan carrot cake muffins with a creamy, dairy-free glaze!

Do you love muffins? Check out more of my easy and nutritious muffin recipes:

More Healthy Breakfast Recipes

Gluten-free carrot cake muffins with cream cheese glaze on a kitchen counter.

Gluten-Free Carrot Cake Muffins and Cream Cheese Glaze

This is the best-tasting Gluten-Free Carrot Cake Muffins and Cream Cheese Glaze Recipe for a delicious breakfast or snack. These healthy muffins are made with almond flour, oat flour, and cassava flour and naturally sweetened with cane sugar, raisins, applesauce, and cottage cheese and topped with cinnamon, toasted coconut, and chopped pecans.
5 from 9 votes
Print Recipe Pin Recipe
Servings 12
Prep Time 20 minutes
Cook Time 25 minutes
Total Time 45 minutes

Ingredients
  

  • 3 eggs
  • 1/2 cup cane sugar
  • 1/3 cup cottage cheese (or sour cream)
  • 1/3 cup unsweetened applesauce
  • 1/3 cup avocado oil (or light olive oil)
  • 2 teaspoons vanilla extract
  • 2 teaspoons apple cider vinegar
  • 1 cup almond flour
  • 1 cup oat flour
  • 2/3 cup cassava flour
  • 2 teaspoons baking powder
  • 1/4 teaspoon baking soda
  • 1 teaspoon cinnamon
  • 1/2 teaspoon salt
  • 1/2 teaspoon ginger
  • 1/4 teaspoon nutmeg
  • 1/2 cup golden raisins
  • 1/2 cup shredded carrots (3 medium carrots)
  • 1/3 cup shredded coconut

Cream Cheese Glaze:

  • 1/2 cup powdered cane sugar
  • 2 ounces cream cheese
  • 2 tablespoons butter
  • 1/2 teaspoon vanilla extract
  • 2 tablespoons almond milk (any milk)
  • 1/2 teaspoon lemon juice

Instructions
 

  • Preheat your oven to 425°F and line a muffin tin with paper liners or lightly grease it.
    Blend the cottage cheese smooth in a food processor, upright blender or chopper cup of an immersion blender to remove the curdled texture.
    In a large mixing bowl, whisk together the eggs, cane sugar, cottage cheese, unsweetened applesauce, avocado oil, vanilla extract, and apple cider vinegar until well combined.
    Add the dry ingredients, including almond flour, oat flour, cassava flour, baking powder, baking soda, cinnamon, salt, ginger, and nutmeg. Whisk until just combined.
    Gently fold in the golden raisins, shredded carrots (3 medium-sized carrots), and shredded coconut with a spatula until combined.
  • Divide the batter evenly among the muffin cups, filling each almost full. Allow the batter to mound higher in the middle for a higher dome.
    BAKING OPTION 1:
    To achieve a higher dome on the muffins, bake at 425°F for 5 minutes. Then, leave the muffin tin in the oven, reduce the heat to 350°F, and bake for 20-22 minutes, or until golden brown and a toothpick inserted into the center of a muffin comes out clean. 
    BAKING OPTION 2:
    Bake 350°F for 25-28 minutes, until golden brown and a toothpick inserted into the center of a muffin comes out clean.
    Allow the muffins to cool in the tin for 5 minutes, then transfer them to a wire rack to cool completely.
  • In a small bowl, beat the powdered cane sugar, room-temperature cream cheese, butter, vanilla extract, almond milk, and lemon juice until smooth and creamy.
    Once the muffins are completely cool, drizzle the cream cheese glaze over each muffin.
    Optional: sprinkle a hint of cinnamon, toasted coconut, and chopped walnuts or pecans on top of the muffins. Allow the glaze to cool and set and enjoy!

Video

YouTube video

Notes

Baking Time: Baking the muffins at a higher temperature and then reducing it will give a heat boost to the muffins, resulting in a higher dome.
Spice Flavor: Adjust the amount of spices to your taste. For an extra flavor kick, add a pinch of cloves or cardamom.
Glaze Consistency: If the glaze is too thick, add more almond milk a teaspoon at a time until it reaches the desired consistency. If it’s too thin, add a bit more powdered sugar.
Toasted Coconut: Adding toasted coconut on top of the muffins is optional but adds flavor and texture! Bring a frying pan to medium heat and melt 1 teaspoon of butter. Add 1/3 cup of coconut and several pinches of salt. Continuously stir the coconut for several minutes until it is lightly toasted.

Nutrition

Calories: 317kcalCarbohydrates: 36gProtein: 6gFat: 17gSaturated Fat: 5gPolyunsaturated Fat: 2gMonounsaturated Fat: 6gTrans Fat: 0.1gCholesterol: 52mgSodium: 271mgPotassium: 148mgFiber: 2gSugar: 20gVitamin A: 1081IUVitamin C: 2mgCalcium: 101mgIron: 2mg
Keyword almond flour, carrot cake, cassava flour, cream cheese glaze, muffins, oat flour
Did you make this recipe and love it?Please let me know in the comments below how it turned out 🙂

11 Comments

  1. Hi Nicole,
    I was wondering if I can substitute the sugar and oil with more natural products. Suggestions? Can I use maple syrup as a substitute and possibly a nut butter for oil?

    Reply

    1. Hi Cindy, those are excellent questions! Yes, you can substitute the granular sugar for maple. I haven’t tried using a nut butter instead of oil. I think the nut butter will be thick and will require some additional liquid to get the same batter consistency. My favorite healthy oils to use are avocado oil and light olive oil. You could decrease the oil by 1 tablespoon and increase the applesauce by 1 tablespoon and still get a delicious result.

      Reply

  3. 5 stars
    I’m a spice cake lover myself so this really hits the spot for me. The carrots, mixed with the raisins, and the frosting all pair together so well.

    Reply

  4. 5 stars
    What a delicious treat! This is such a fun way to have carrot cake that still leaves you feeling satisfied😊

    Reply

  5. 5 stars
    these are incredibly moist and light! I did not expect that from a GF muffin. Thank you for an easy an awesome recipe.

    Reply

  6. 5 stars
    I’m excited to share this healthier carrot cake muffin recipe with you! Please let me know if you have a chance to make it 🙂

    Reply
5 from 9 votes (4 ratings without comment)

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