Gluten Free Carrot Zucchini Muffins

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These gluten free carrot zucchini muffins are low carb, refined sugar free, and full of fresh veggies. The perfect morning snack!

Carrot Zucchini Muffins #glutenfree and can easily be made #grainfree too. Full of protein and veggies they make a great breakfast!

I have a sweet spot for muffins in my stomach. Muffins were one of the first things I learned to bake when I was a little girl. Which I guess I say a lot, but pumpkin chocolate chip muffins really were a staple in our home and I loved making them with my mom. Measuring and adding ingredients, stirring the batter, and licking the bowl of course.


These gluten-free carrot zucchini muffins are easy enough that you can make them with your kiddos if they want to help. Miss E loves helping me in the kitchen. I think she really spent more time playing with a whole carrot on a cutting board and dumping the salt shaker all over the floor than helping me  make muffins but it is all about the experience.

Carrot Zucchini Muffins #glutenfree and can easily be made #grainfree too. Full of protein and veggies they make a great breakfast!

She is also quite the budding food stylist. If you follow me on Instagram you probably saw this picture of her rearranging all of the “cupcakes” for me.  She loves helping mommy! (If you don’t follow me on Instagram, you should. All the behind the scenes and previews of what I’m baking. )

Carrot Zucchini Muffins #glutenfree and can easily be made #grainfree too. Full of protein and veggies they make a great breakfast!

Muffins make a great breakfast or snack but often times they are loaded with sugar. Which of course never stops me from eating them. I just wanted to create a gluten-free recipe that was going to fill my 28 week pregnant body with some nutrients and protein instead of giving my baby a sugar high. I really didn’t miss the refined sugar in these gluten-free muffins at all.

Carrot Zucchini Muffins #glutenfree and can easily be made #grainfree too. Full of protein and veggies they make a great breakfast!

They are slightly sweet and extra moist from the honey, freshly shredded zucchini and carrot for some fiber and nutrients, protein from the almond flour, a little rice flour to lighten up the texture, and whipped cream cheese to top them off.

Carrot Zucchini Muffins #glutenfree and can easily be made #grainfree too. Full of protein and veggies they make a great breakfast!

If you want to avoid grains entirely instead of just doing it gluten-free you can try using an extra half a cup of almond flour instead of the rice flour. The muffins won’t be quite as light, but will still be delicious!

Carrot Zucchini Muffins
Prep time
Cook time
Total time
Sweet Carrot Zucchini Muffins are gluten-free and low carb. They make a great protein-filled breakfast! You can even top them with cream cheese "frosting."
Recipe type: Muffin
Serves: 1½ dozen
  • 1½ cups almond flour
  • ½ cup brown rice flour
  • 2½ teaspoons baking powder
  • ½ teaspoon salt
  • 1 teaspoon cinnamon
  • ½ cup honey (or pure maple syrup)
  • ½ cup oil (vegetable or coconut)
  • 2 eggs
  • ½ cup finely shredded carrots
  • 1¼ cups finely shredded zucchini
For the "Frosting"
  • 8 oz cream cheese, softened
  • 1-2 tablespoons honey
  1. Preheat your oven to 350F. Line a muffin tin with paper liners, or liberally grease.
  2. In a mixing bowl combine the almond flour, brown rice flour, baking powder, salt, and cinnamon.
  3. Make a "well" in the dry ingredients and add the honey, oil, and eggs and stir to combine. The batter will be thick. Add the shredded carrots and zucchini and stir until they are evenly distributed.
  4. Fill each muffin liner with better so it is about ¾ full.
  5. Bake for 30-35 minutes or until the edges are golden and the muffin springs back if you lightly touch it.
  6. Let cool before frosting, if desired.
For the frosting...
  1. Whip the cream cheese until light and fluffy using an electric stand or handheld mixer. Add the honey and continue to whip until combined.
You can easily use more carrot and less zucchini, or even all zucchini if you want. Just make sure the total amount of shredded vegetables in the recipe is the same.


Some other scrumptious muffin recipes from yours truly…

Gluten-Free Chocolate Chocolate Chip Muffins

Gluten-Free Chocolate Chocolate Chip Muffins

 Gluten-Free Cranberry Chocolate Muffins

Gluten-Free Cranberry Chocolate MuffinsGluten-Free Pumpkin Chocolate Chip Muffins

Gluten-Free Pumpkin Chocolate Chip Muffin


Linked up at Gluten-Free and DIY Tuesday, Allergy Free Wednesday, and Gluten-Free Wednesday


    • flippindeliciousflippindelicious says

      Lacy that is a great idea! I think I’m going to have to get some zucchini while it is in season and save it in the freezer just for these muffins.

  1. says

    Carrots and zucchinis! I have plenty of both in my vegetable garden and your recipe is what I was looking for! Thanks for sharing (and I will let you know how they turned out as soon as I try them).:-))

    • flippindeliciousflippindelicious says

      Thanks Barbara! Now is the best time for these muffins because everyone seems to have extra carrots and zucchini on hand. I hope you enjoy them!

    • Hany says

      Muffins are like by all kinds of age groups and pelpoe would just love to eat them. Such a good dish. This dish is unique.Good one.

    • flippindeliciousflippindelicious says

      Emily, the recipe will not work exactly the same if you use regular flour since almond flour and rice flour both work very differently than wheat flour. That being said you may still be able to use wheat flour but you may need more or less (you probably can’t substitute it straight across). Because wheat flour has gluten in it you’ll have to be very careful to not over-stir the batter because it will get very tough if you stir it too much.

    • flippindeliciousflippindelicious says

      Stacie, for this specific recipe a GF all-purpose flour may not work. At least for the almond flour. You could definitely use a blend instead of the rice flour in the recipe. Almond flour bakes very differently from AP blends. You can probably still make similar muffins with GF AP flour, you’d just have to experiment with the amounts. If you try it let me know!

    • flippindeliciousflippindelicious says

      John I would probably substitute the rice flour with more almond flour. The finished muffin may not be as light, but will still be delicious and will have even more protein! You could also try substituting half arrowroot and half almond flour which might make the muffin less dense. If you try any substitutions please let me know, I’d love to know how it turns out.

  2. shirley anne peacock says

    these sound amazing 🙂 i can’t tolerate almond flour, could i use coconut flour to replace it? also what other gf flour could i replace the rice flour with? or could i just use more coconut flour? thank u 🙂

    • flippindeliciousflippindelicious says

      Hi Shirley,
      If your body can tolerate another nut flour that would transition the easiest. If you try coconut flour please let me know how it turns out. I know that coconut flour bakes very differently than other flours so you may need to change the amount of flour in the recipe.
      If you are looking to replace the rice flour also I’d choose something with a mild flavor and similar consistency. Maybe millet? Or a white sorghum?
      Let me know what you try and how it turns out!

      • shirley anne peacock says

        Great thank u for the quick reply. i will just try to use coconut flour on its own and increase the amount of eggs! I like the taste of coconut and i have been making chocolate brownies with zucchini and they turn out soooo good. x

  3. Rosemary says

    Hi – made these yesterday – nice taste – but I would add that if you beat the cream cheese too much it will go too soft and liquidy, therefore will not hold it’s shape. Better to just fold in the honey. Or else just make a buttercream icing to pipe on top.

  4. dee says

    these are fabulous! everyone loved them. Note: you need to squeeze out all the extra liquid from the shredded zucchini first. these will be a constant in my family baking.

    • flippindeliciousflippindelicious says

      Hi Elieen,
      For this specific recipe there isn’t a flour blend that I’d recommend substituting. This recipe was specially formulated for almond flour, which bakes very differently than other flours. Sorry!
      If you do try substituting a different flour please let me know how it turns out.

    • flippindeliciousflippindelicious says

      Hi Emily,
      I recommend brown rice flour or similar. Both oat and coconut flour work differently and I don’t know how they’d turn out. If you try it leave a comment so that other readers will know if it worked for you. Happy Baking!

  5. Jaime says

    I just made these, and used duck eggs instead, but the batter was soooooo dry. I added some almond milk and more honey, and it was still dry. I hope they turn out!

    • flippindeliciousflippindelicious says

      Whenever you deviate from the recipe there is always a risk things will turn out differently. I’ve never used duck eggs so I have no idea how that would effect the finished muffins.

  6. rebecca says

    Help my muffins came out Brown like almost too brown on top and hallow and squishy on the inside. What did I do wrong? I believe I followed the recipe. I may have more grated than shredded my carrot and zuch.

    • flippindeliciousflippindelicious says

      Rebecca, if it was too wet and “squishy” inside it probably has to do with the moisture in the muffins. You have to squeeze out the extra moisture in the carrot and zucchini, you can’t get it all but you want to get most of it. Having extra moisture in the muffins makes it to you have to bake them longer, which can cause it to brown too much. Because they browned too much on the top I’d try baking them at a lower temperature, for longer. That way they can bake all the way through before the top starts to brown. By lowering the temperature hopefully the top won’t get as brown.
      There could also be a problem with how your oven heats. It could be baking unevenly. It is hard to know exactly what went wrong without being there but hopefully this gives you a few places to start.

  7. says

    Brianna! I have made these a couple of times now and the whole family digs them!, we leave the brown rice flour out and use tapioca to replace it. I also use palm sugar in place of the honey and use a touch of stevia too. I purée all the wet ingredients in the blender first, then add e dry in on top….works like a charm! And then I do not have to grate any veggies and worry about my youngest Turing his nose up at visible vegetable!

    • flippindeliciousflippindelicious says

      Yay! I’m so happy to hear that Tessa! Blending the batter is a great idea, I have some picky veggie kids too. Plus, it sounds so much easier.

  8. Carley says

    I just made these and they turned out horrible. I sprayed my muffin tins and oven was at the right temp. They burnt and are soggy in the middle. They also didn’t rise at all. Very disappointed. In the bin they go.

    • flippindeliciousflippindelicious says

      Hi Carley! I am sorry that they didn’t turn out for you. Do you use a thermometer inside of your oven? My oven often runs 25-30 degrees hot,so I don’t ever rely on the temperature that my oven says it is. If your oven runs hot that very likely could have been the problem. If you try them again just lower the temperature of your oven and bake them until a toothpick comes out clean.
      There also could have been too much liquid in your batter if you didn’t squeeze the liquid out of your zucchini and carrots. That also could have caused them to be soggy in the middle.
      Hope that helps!

  9. Ashley says

    Hello 🙂 This was my first attempt at a gluten free recipe and I was so exited. I cooked them for less time since I’m in high altitude and they came out burnt. I decided to taste them anyway and the middle seemed way too moist, a little raw 🙁 I don’t know what I did wrong, any thoughts? I bake all of the time but maybe I was having an off day or something. Thank you for any feedback.

    • flippindeliciousflippindelicious says

      Hi Ashley, I am sorry, without being in the kitchen along side you I can’t tell what went differently for you. I am also at a high altitude, so I don’t think that would be it. Oven temperatures vary, also if you didn’t squeeze out enough of the liquid from the zucchini and carrots it could cause them to be too wet.

    • flippindeliciousflippindelicious says

      Hi Terry, I’m sorry, I do not. In the past I’ve used My Fitness Pal to calculate counts for my personal use. I’d suggest using their app, or your favorite. I hope to have more nutrition information on my site in the future.

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