These healthy zucchini carrot muffins are made with almond flour, packed with veggies, and very lightly sweetened with honey. They're perfect for a snack or quick breakfast and are SCD, paleo, gluten free, grain free, dairy free, and refined sugar free.

These delicious gluten free almond flour zucchini carrot muffins are spiced with cinnamon, nutmeg, and cardamom while being very lightly sweetened with honey.
The SCD muffins (my first ever on the blog) are fluffy and a great way to sneak in some extra veggies while still enjoying a baked treat!
Ingredients
Almond Flour - I recommend using blanched finely ground almond flour and almost always use the Kirkland brand from Costco.
Honey - These muffins are not very sweet at all. This is done on purpose so that you can add jam, butter, drizzled honey, etc. without having overly sweet muffins. However, if you prefer sweeter muffins, increase the honey to ½ cup.
Zucchini - Yellow squash or a combination of zucchini and yellow squash can be used.
How to make the healthy zucchini carrot muffins
Begin by shredding zucchini. Place on a thin tea towel and sprinkle with salt (photo 1). Set aside for 10 minutes.
While you're waiting on the zucchini, go ahead and shred the carrots.
In a large bowl whisk together the dry ingredients (photo 2).
In a separate bowl whisk together the wet ingredients (photo 3).
Then pour the wet ingredients into the bowl of dry ingredients and whisk until well combined (photo 4).
At this point the batter will be very thick (photo 5). Do not freak out and add more liquid. While the muffins are baking the carrots and zucchini will add extra moisture.
Wrap the zucchini in the tea towel and squeeze out as much liquid as possible.
Just when you think there can't possibly be anymore liquid left, squeeze again (photo 6)!
Once you're satisfied that you've removed as much moisture as possible, add the zucchini and shredded carrots to the bowl (photo 7).
Use a rubber spatula to mix the batter (photo 8).
Evenly distribute the batter between 12 lined muffin cups (photo 9) and bake until the tops are a light golden color and a toothpick inserted into the center of the muffins comes out clean.
Preparing the zucchini for baking
Zucchini naturally has a very high water content which, when used in baked goods, can translate to a very soggy bake.
To avoid this, it's important to allow the shredded zucchini to "sweat" by placing on a thin tea towel and after 10 minutes, squeezing out as much liquid as possible.
This step is critical, so don't skip it!
How to store the muffins
The zucchini muffins can be stored in an airtight container on the counter for up to 3 days, or in the refrigerator for up to 5 days.
If you'd like to freeze the muffins, begin by removing the paper liner.
Wrap each muffin individually with plastic wrap, then wrap the muffins again using aluminum foil.
Store in a ziploc bag in the freezer for up to 3 months.
Muffins can be thawed in the refrigerator overnight or on the kitchen counter for a few hours.
More healthy things to bake!
- Almond Flour Zucchini Bread
- Prosciutto Egg Cups
- Savory Summer Squash Waffles
- Healthy Banana Bread Muffins
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NOTE: If following the SCD diet, I suggest contacting the company to verify ingredients before using any prepackaged products.
Recipe
Healthy Zucchini Carrot Muffins
Ingredients
- 1 medium zucchini, shredded (about 1 cup)
- 2 medium carrots, shredded (about 1 cup)
- 3 cups blanched finely ground almond flour
- 1 Tablespoon ground cinnamon
- 1 teaspoon fine sea salt (plus more for shredded zucchini)
- 1 teaspoon baking soda
- ¼ teaspoon ground nutmeg
- ⅛ teaspoon ground cardamom
- 3 large eggs, at room temperature
- ⅓ cup honey
- 2 Tablespoons orange juice
- 2 Tablespoons olive oil
- 2 teaspoons vanilla extract
Instructions
- Preheat oven to 325F. Line 12 cups of a standard muffin pan with liners and set aside.
- Shred the zucchini onto a thin tea towel and sprinkle with some salt. Set aside and allow to "sweat" for 10 minutes. Shred the carrots and set aside.
- In a large bowl whisk together the almond flour, salt, baking soda, cinnamon, nutmeg, and cardamom.
- In a separate bowl whisk together he eggs, honey, orange juice, olive oil, and vanilla. Then pour the mixture into the bowl of dry ingredients. Whisk until well combined.
- Wrap the zucchini in the tea towel and squeeze out as much liquid as possible. Place 1 cup of the zucchini and 1 cup of the shredded carrots into the batter. Use a spatula to mix.
- Evenly distribute the batter among the muffin cups, filling until about ¾ths full.
- Place the muffin pan on the center rack of the oven and bake for 25 to 30 minutes or until the tops of the muffins are a golden color and a toothpick inserted into the center comes out clean.
- Allow to cool for 10 minutes before turning out onto a wire rack to cool completely.
Notes
- These muffins are not very sweet. If you prefer a sweeter muffin, then increase the honey to ½ cup.
- Muffins can be stored for up to 3 days covered at room temperature or up to 5 days in an airtight container in the refrigerator.
- The zucchini carrot muffins can also be frozen for up to 3 months.
Nutrition
You can also check out my web story for these Healthy Zucchini Carrot Muffins!
Liliana
Is it possible to sub with oat flour? My little one is allergic to nuts.
ayleen ford
First time baking in my life. Easy to make, great instructions and easy to follow. Great flavor. I enjoyed them without affecting my glucose levels. Thank you
Rose
Hi Jennifer,
Second time making these muffins, So Delicious!
Rose
Jennifer Brown
Glad you like them! Thanks so much for taking the time to leave a review, I really appreciate it!
Julie Edwards
These were delicious! I did add more honey 1/2 c, 1/2 c chopped pecans and 1/2 c chopped dates! They turned out delicious!
Jules
These muffins are absolutely wonderful ❤️ The perfect level of sweetness for my family. I used coconut oil instead of olive and made 13 beautiful muffins, filled all the way to the top 😁 Loved it! Thank you for the excellent recipe!
Deanna
Hi! I want to make these muffins in a day or two. May I substitute egg whites for the whole eggs in the recipe? Also, how about substituting Stevia added to a little water instead of the honey? Lifelong diabetic here. Thank you so much! I look forward to trying these muffins.
Jennifer Brown
Unfortunately I haven't tried using egg whites or stevia in this recipe so I'm not sure how they will turn out, but f you decide to experiment please come back and let us know how they turned out.
sherri
Excellent!! No weird texture, nice and moist. I made it in "cake" form and added ginger and cloves (since I didn't have cardamon) and it was great. Even my family likes them and so healthy! Thank you for the recipe!
Jennifer Brown
So happy you all enjoyed it!
Marisa
Can you make this into a bread too?
Jennifer Brown
Yes you can! If using a 10 inch loaf pan it should take around 50 to 60 minutes to bake.
Susan
I love them. I didnt have cardamom so i use grounds cloves and it end up really good.
Sandy
Best healthy muffin recipe I've tried. Thank you!
Jennifer Brown
I'm glad you enjoyed them Sandy!
EIL
I didn't have OJ, but I did have OJ
infused cranberries from Trader Joes. Excellent gluten free!
Jennifer Brown
Glad you enjoyed them!
Pooja
Hi Jen,
Can I replace orange juice with lemon juice? Has anyone tried this?
Thanks
Jennifer Brown
Yes you can!