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    Home > Recipe Index > Baked goods/breads > Gluten Free Carrot Cake Muffins Recipe with Maple Cream Cheese Frosting (Paleo Friendly!)

    Gluten Free Carrot Cake Muffins Recipe with Maple Cream Cheese Frosting (Paleo Friendly!)

    Published: Mar 31, 2021 · Modified: Nov 19, 2022 by Nicki Sizemore · This post may contain affiliate links

    Jump to Recipe Print Recipe
    Two frames, one showing carrot cake muffin batter in a Vitamix and the other showing a healthy carrot cake muffin with a bite taken out.
    Two frames, one showing carrot cake muffin batter in a Vitamix and the other showing a healthy carrot cake muffin with a bite taken out.

    These healthy, gluten free carrot cake muffins are my new obsession. They’re delicious just as they are, but downright incredible when slathered with a maple cream cheese frosting. AND (drum-roll, please) you don’t even need to break out your mixing bowls to make them. That’s right, friends; these are the EASIEST carrot cake muffins you’ll ever make!

    Close up of a gluten free carrot cake muffin with a bite taken out.

    Gluten free carrot cake muffins

    The muffins are made with a base of almond flour and coconut flour, making them gluten free and grain free. They're also naturally sweetened with maple syrup and can easily be made paleo (see below). With carrots, raisins, nuts and warming spices, these are healthy carrot cake muffins that taste just like the original.

    All of the ingredients for the carrot cake muffins arranged on a work surface and labeled.

    Carrot cake muffins in the Vitamix

    Even better, the muffins get made entirely in the Vitamix or food processor! That means NO shredding of carrots and NO mixing bowls - the Vitamix handles everything from the chopping of carrots to the mixing of the batter (woot woot!). They're a cinch to make, and clean-up is a breeze.

    Process shot showing chopped carrots in a Vitamix blender.
    Process shot showing the carrot cake muffin batter in a Vitamix blender.

    Healthy cream cheese frosting

    While the muffins are delicious on their own, you can slather them with a Healthy Cream Cheese Frosting if you want to take them over the top. MEANING IT WILL FEEL LIKE YOU'RE EATING CUPCAKES FOR BREAKFAST!

    That last part got me a little excited.

    Hand blender mixing the maple cream cheese frosting in a bowl.

    Paleo carrot cake muffins

    For paleo carrot cake muffins, simply omit the frosting or top the cupcakes with maple-sweetened coconut whipped cream instead!

    Paleo carrot cake muffins on a cooling rack.

    FAQs

    How should I store carrot cake muffins?

    The unfrosted muffins can be stored in an airtight container at room temperature for up to 3 days, or frozen for up to 3 months. Once frosted, the cupcakes can be refrigerated for up to 3 days.

    How do I make carrot cake muffins in a Vitamix?

    First, finely chop carrots in a Vitamix, then transfer to a bowl. Add the wet ingredients to the Vitamix and blend. Sprinkle in the dry ingredients and pulse to incorporate. Stir in the chopped carrots, raisins, and nuts, if using.

    What if I don't have a Vitamix?

    You can make these carrot cake muffins in a food processor instead! Follow the same instructions.

    Healthy carrot cake muffins topped with maple cream cheese frosting, with a knife alongside.

    Gluten free carrot cake muffin tips:

    • When baking muffins it’s best to use a light colored pan, as dark pans can cause the bottoms and sides to darken too quickly.
    • I prefer to cook these muffins in oiled pans, but you can use paper liners if you prefer. Just be sure to let the muffins cool completely, otherwise they might stick to the liners.
    • I highly recommend investing in a kitchen scale, especially when working with gluten free flours. They’re not very expensive, and they make baking much easier (no measuring cups to wash!) and far more accurate (meaning better baked goods!).
    • I use Bob’s Red Mill almond flour and coconut flour, since they’re easy to find, affordable and reliably fresh.
    • If you don’t have a Vitamix you can use a Food Processor.
    • To take the muffins over-the-top, slather them with this Maple Cream Cheese Frosting.
    • If it's an actual cake you're after, don't miss this Healthy Carrot Cake Recipe!

    *This post contains Amazon and other affiliate links to products I use and love (from which I earn income, at no cost to you). Thank you or supporting From Scratch Fast!

    Close up of a carrot cake muffin topped with cream cheese frosting and chopped pecans.

    Other healthy breakfasts and snacks to try:

    • Blueberry Blender Muffins
    • Banana Oatcakes
    • Baked Oatmeal Bars
    • Paleo Pumpkin Bread
    • BEST Gluten Free Banana Bread
    • Banana Oat Blender Pancakes
    • Banana Oat Breakfast Cookies
    • Pumpkin Spice Breakfast Cookies

    *Thank you to Vitamix for sponsoring this post! I was compensated for this post, but all opinions and recipes are my own.

    Watch the Video!

    Stay connected!

    I'd love to answer any of your questions and see what you're cooking!! Don't forget to rate this recipe and leave a comment below. Follow along on Instagram, Facebook, YouTube & Pinterest, and be sure to tag @fromscratchfast so that I can share your creations!

    Get the Recipe!

    Gluten free carrot cake muffins with cream cheese frosting on a cooling rack.
    Print Recipe Pin Recipe

    Gluten Free Carrot Cake Muffins with Maple Cream Cheese Frosting (Paleo Option))

    These healthy, naturally sweetened carrot cake muffins are gluten-free, grain-free, and are packed with carrots, but who cares, because THEY TASTE JUST LIKE CARROT CAKE! Oh, and did I mention that they get slathered with a Maple Cream Cheese Frosting?! (You'll only need a half batch of the frosting.) Best of all, the batter gets made entirely in the Vitamix or in a food processor. I encourage you to use an inexpensive scale when making these muffins—it’s not only easier (you won’t have to mess with a ton of measuring cups) but it’s also far more accurate. Be sure to check out my other muffin making tips above! These muffins are even better the next day, after all of the flavors have had time to meld.
    Prep Time20 mins
    Cook Time35 mins
    Total Time55 mins
    Course: Breakfast, Dessert
    Cuisine: American
    Keyword: carrot cake muffins, easy carrot cake muffins, healthy carrot cake recipe
    Servings: 11 Muffins
    Author: Nicki Sizemore

    Ingredients

    • Coconut oil or cooking spray for muffin tins
    • ½ cup (70 g) raisins
    • 3 medium carrots (220 g), peeled, trimmed and coarsely chopped
    • 3 large eggs
    • ¼ cup (80 g) maple syrup
    • ¼ cup coconut oil (48 g), melted and cooled slightly
    • 2 tablespoons unsweetened nut milk or regular milk
    • 2 teaspoons fresh lemon juice
    • 1 teaspoon grated fresh ginger
    • 1 teaspoon vanilla extract
    • 1 ¼ cup (125 g) finely ground almond flour
    • ¼ cup (25 g) coconut flour
    • ¼ cup (25 g) shredded unsweetened coconut
    • 2 teaspoons cinnamon
    • ⅛ teaspoon freshly grated nutmeg
    • ¾ teaspoon baking soda
    • ½ teaspoon fine sea salt
    • ⅓ cup (38 g) chopped walnuts or pecans, optional
    • ½ batch Maple Cream Cheese Frosting (optional), recipe link in header

    Instructions

    • Preheat the oven to 350˚F. Grease 11 muffin cups generously with coconut oil or cooking spray.
    • Cover the raisins with warm water and let sit.
    • Place the carrots in the Vitamix or food processor. If using the Vitamix, turn the machine on and gradually increase to medium speed (Variable 6 or 7), stirring with the tamper. Blend until the carrots are very finely chopped (it will only take a few seconds). If using the food processor, pulse the carrots until very finely chopped. Transfer to a bowl.
    • Place the container back on the base (no need to wash it—it’s ok if there are still some carrots around the edges and bottom), and add the eggs, maple syrup, coconut oil, milk, lemon juice, ginger and vanilla. Blend until smooth.
    • Sprinkle in the almond flour, coconut flour, coconut, cinnamon, nutmeg, baking soda and salt. Blend on low (Variable 2 or 3) or pulse (if using a food processor) until incorporated.
    • Drain the raisins, and add them to the batter along with the chopped carrots and nuts (if using). Blend on low (Variable 1), stirring with the tamper, or pulse if using a food processor, until just incorporated. Using a rubber spatula, scrape the sides and stir to fully incorporate all of the ingredients.
    • Scoop the mixture into the prepared muffin cups (an ice cream scoop works great for this). Bake 30-35 minutes, until the muffins are golden on top and a toothpick inserted in the center comes out clean. Cool in the tin for 5 minutes, then transfer the muffins to a cooling rack and let cool completely. 

    Notes

    Make it Ahead: The unfrosted muffins can be stored in an airtight container at room temperature for up to 3 days, or frozen for up to 3 months. Once frosted, the cupcakes can be refrigerated for up to 3 days.
    Tips:
    • When baking muffins it’s best to use a light colored pan, as dark pans can cause the bottoms and sides to darken too quickly.
    • I prefer to cook these muffins in oiled pans, but you can use paper liners if you prefer. Just be sure to let the muffins cool completely, otherwise they might stick to the liners.
    • I highly recommend investing in a kitchen scale, especially when working with gluten free flours. They’re not very expensive, and they make baking much easier (no measuring cups to wash!) and far more accurate (meaning better baked goods!).
    • I use Bob’s Red Mill almond flour and coconut flour, since they’re easy to find, affordable and reliably fresh.
    • If you don’t have a Vitamix you can use a Food Processor.
    • To take the muffins over-the-top, slather them with this Maple Cream Cheese Frosting (you'll only need a half batch). 
    • If it's an actual cake you're after, don't miss this Healthy Carrot Cake Recipe!

    Stay Connected!

    I’d love to hear what you’re cooking, and I’m happy to answer any questions! #FromScratchFast

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    This post contains affiliate links, which means that if you purchase a product through a link you clicked on here, I receive a portion of the sale (at no cost to you). Thank you for supporting FromScratchFast!!

    More Baked goods/breads

    • Easy Gluten Free Baked Donuts Recipe (No Yeast!)
    • Easy Maple Glaze (for donuts, scones, cakes and more!)
    • Gluten Free Zucchini Bread (Naturally Sweetened, Dairy Free)
    • Easy Gluten Free Vegan Flatbreads (No Yeast Naan Bread!)

    Reader Interactions

    Comments

    1. Genevieve says

      January 03, 2022 at 6:41 pm

      Hi! I saw that the carrot cake uses baking powder, while the muffins use baking soda. I was just wondering if there might be a mistake, or it's just different since one is a cake and the other is a muffin.

      I like your carrot cake video by the way!

      Reply
      • Nicki Sizemore says

        January 05, 2022 at 1:17 pm

        Hi Genevieve, great question! I developed the muffin recipe several years ago and used baking soda, which needs acid to activate (hence the lemon juice). When I developed the carrot cake recipe I simplified and streamlined things a bit, using just baking powder, which doesn't need acid to activate. I hope you enjoy (and thank you about the video!).

        Reply
        • Genevieve says

          January 06, 2022 at 11:11 pm

          Oh, OK. Thank you so much. I really appreciate your explanation. I can learn a lot from you!

    2. Anna says

      July 31, 2021 at 11:32 am

      5 stars
      Thank you for the recipe. These were wonderful. I made them with my 7 year old niece who had fun lining up all TWENTY ingredients clear across the countertop. Whew, what a miracle!

      Reply
      • Nicki Sizemore says

        August 01, 2021 at 8:27 am

        Hi Anna, I'm so happy you and your niece liked the muffins (and I LOVE that she's such a little sous chef! 😂).

        Reply
    3. Debra says

      May 22, 2020 at 10:49 am

      Hi, have you tried this recipe in a cake pan or square pan? If yes, what size and bake time. Thank you. I’m new to a dr recommended GF diet and your recipes have helped to make my GF food family friendly too — at least no complaints, yet!

      Reply
      • Nicki Sizemore says

        May 26, 2020 at 3:40 pm

        Hi Debra, stay tuned because I have a healthy carrot cake recipe coming soon (it's very similar to this but with a couple tweaks for texture), and it gets made in an 8-inch square pan!! I'm so happy your family is liking the recipes! 🙂

        Reply
    4. Lillian says

      April 10, 2020 at 1:07 am

      Since we are all supposed to stay home I only have unbleached flour and oat flour..... can I sub with one or the other or both?

      Reply
      • Nicki Sizemore says

        April 10, 2020 at 8:49 am

        Hi Lillian, I hope you are staying safe and well! Unfortunately I haven't tested these muffins with all-purpose flour or oat flour so cannot guarantee the results. Unbleached flour might work, but again, it has not been tested. Definitely let me know if you give it a try!

        Reply
    5. Dini says

      April 03, 2020 at 10:01 am

      I'm excited to try these this weekend! My kids don't like raising (crazy!) so I was thinking of subbing with dried cranberries. My coconut flakes are already sweetened, too so I was thinking of reducing the sugar a bit. Sounds ok? Any flags for doing that?

      Reply
      • Nicki Sizemore says

        April 03, 2020 at 1:15 pm

        Hi Dini, let me know how you like the cranberries! We often use currants in place of the raisins. I would keep the same amount of sweetener (1/4 cup maple syrup), but cut back on the coconut slightly (try 3 tablespoons of the sweetened coconut). Let me know how they turn out!

        Reply
    6. MJ says

      August 18, 2019 at 10:21 pm

      5 stars
      These taste sooo good! Thank you for the recipe. I made them a few times now and they were a big hit. Do you think I could use whole wheat flour instead of almond flour?

      Reply
      • Nicki Sizemore says

        August 19, 2019 at 9:40 am

        I'm so happy that you like the muffins!! I suspect that using whole wheat pastry flour in place of the almond flour and coconut flour would work. (Using pastry flour, which has a lower gluten content than regular flour, would help retain a delicate crumb.) However, I've never tested these with wheat flour so it would be a bit of an experiment. If you try it please report back! Thank you, and happy baking!

        Reply
    7. Jenni says

      February 28, 2018 at 3:46 am

      Have you tried this recipe with the egg substitute aquafaba?

      Reply
      • Nicki Sizemore says

        March 16, 2018 at 6:48 pm

        I've never tried these with aquafaba but now am curious! I suspect "flax eggs" would also work if you're looking to make these egg-free.

        Reply
    8. BEthany says

      May 11, 2017 at 5:02 pm

      Oh! These muffins look delicious!

      Reply
      • Nicki Sizemore says

        May 12, 2017 at 12:51 am

        Thank you!! 🙂

        Reply

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    Meet Nicki

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    Welcome! I’m Nicki Sizemore, a trained chef, recipe developer and cookbook author. My mission is to help you make wholesome & delicious food from scratch without spending hours in the kitchen. All of my recipes are naturally gluten-free.

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