Zucchini Apple Muffins (Gluten/Grain-free, Paleo, SCD-legal)

Zucchini Apple Muffins (Gluten/Grain-free, SCD Legal, Paleo) | This is so good...I’m so blessed to have a bumper crop of garden zucchini this year!  Everyday I am picking a couple, so coming up with creative ways to use them is on the top of my list.  I’ve already made my most popular recipe, Coconut Flour Zucchini Bread, several times and made a of batch of Zucchini Banana Muffins.  It was while I was mixing together the ingredients for the muffins that I started thinking about how the recipe could be switched up a bit and I decided to try making Zucchini Apple Muffins.  I’m happy to say the experiment was a success!

These muffins are lightly spiced with cinnamon and have a nice crumbly texture.  The apple chunks are the perfect compliment to the zucchini.  I added another layer of apple flavor by using some homemade applesauce that I canned last year, but this recipe will work just as well with a clean, store-bought version.

We enjoyed these Zucchini Apple Muffins for breakfast and for dessert.  They are delicious warmed with some butter, but are also great at room temperature or cold.

Zucchini Apple Muffins (Gluten/Grain-free, SCD Legal, Paleo) | This is so good...This recipe makes 12 muffins, which in this house, means they won’t be around very long.  However, did you know you can freeze gluten-free baked goods for meals at a later date?  Just wrap them up in plastic wrap (*gasp* I know, I know.  It’s one of the only plastic products I still use) and put them in the freezer.  When you are ready to enjoy a Zucchini Apple Muffin, pull it out, unwrap it and let it thaw.  If you would like to warm it or crisp it up a bit, put it in the toaster oven or a few minutes.

A quick note on my favorite products used to make Zucchini Apple Muffins:

These muffins are made with blanched almond flour.  This is not the same thing as almond meal.  This is my favorite brand of blanched almond flour and the one I used when developing this recipe.

I find that gluten-free baked goods tend to stick to baking pans, even when I grease and flour the pans.  As a work around, I found these unbleached parchment liners that work like a dream!

Let’s get to the recipe!

Zucchini Apple Muffins (Grain-free, Gluten-free)
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  1. 3/4 cup of applesauce (homemade or a clean store bought version)
  2. 3 eggs
  3. 1 teaspoon vanilla (leave out for SCD)
  4. 1-2 Tablespoons raw, local honey (optional if you like a sweeter muffin, I usually leave it out)
  5. 8 ounces (about 2 cups) of blanched almond flour
  6. 2 Tablespoons coconut flour
  7. 1/4 teaspoon sea salt
  8. 1/2 teaspoon baking soda
  9. 2 teaspoons cinnamon
  10. 1 teaspoon apple cider vinegar
  11. 1 heaping cup of shredded zucchini (Place in a clean, dry dish towel and squeeze out as much liquid as possible.)
  12. 1 medium size organic apple, diced into 1/4 inch chunks (I did not peel mine, but feel free to peel before dicing if prefer)
  1. Preheat your oven to 350 degrees and place parchment muffin liners into your muffin tin.
  2. In a bowl, combine the applesauce, eggs, vanilla, and honey (if using). Mix well.
  3. In a separate bowl, combine the almond flour, coconut flour, sea salt, baking soda, and cinnamon.
  4. Pour the wet ingredients into the dry. Add in the apple cider vinegar, diced apples, and shredded zucchini. Mix well.
  5. Portion out the batter into 12 muffin liners.
  6. Bake for 25-28 minutes - until a toothpick inserted into the middle of the muffin comes out clean.
  7. Remove from the oven and let the muffins cool in the pan for 5 minutes. Then remove from the pan and continue to cool on a cooling rack.
  8. Store any left over muffins in an airtight container in the refrigerator or wrap individually in plastic wrap and freeze.
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Do you have an abundance of zucchini?  What is your favorite way to use it?  Tell me in the comments!


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  1. Beautiful recipe. Already pinned and shared!

  2. This looks so great! I do have an abundance of zucchini and have made carrot zucchini bread with cinnamon lemon marshmallow fluff, zoodles, and zucchini chips (in the dehydrator). Yum!!

  3. These look delicious! Shared them and pinned. Looking forward to making some.

  4. These sound divine! I have so much zucchini right now I don’t know what to do with it all! Muffins are always a great choice 🙂

  5. These look delicious! Such a nice texture. I like baking with homemade applesauce as well. Thanks!

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  8. Is it supposed to be 1C or 2C of almond flour? It says 8 oz but then it says 2C, which is 16 oz. Thanks for clarifying!

    • Hi! Thanks for the question. Use two cups of almond flour which is about 8 ounces when weighed, not volume. Sorry for the confusion! Enjoy!!

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  11. Do these freeze well? I usually freeze extra muffins made from coconut flour but I’ve never tried freezing an almond flour version.

    • Hi Rachael,
      I honestly have not tried freezing muffins from this recipe. I have frozen other baked goods made with almond flour and they are fine after a quick toast in the oven. Let me know if you try it!! Thanks for checking out the recipe!

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  13. I need a little help troubleshooting here. I made these today and they didnt come out right. The tooth pick came out clean after cooking for 30 min. BUT, the muffins were still raw in the centers.

    • Hi Brie,
      Sorry that you had trouble with the recipe. Did you really squeeze the zucchini to remove the liquid? If you did, it’s possible that the applesauce you used had a higher water content than mine. Almond flour baked goods tend to be fairly soft in the center, but should not be raw. If you try again with the same ingredients, maybe add a touch more coconut flour.

  14. This looks promising for my 8 yo daughter who is on SCD diet…thank you! What is difference between blanched and unblanched. I only have the unblanched version and wondering if I could use that instead.

    • Hi! I believe unblanched flour still has the almond skins in there. I’m not sure how this would effect the recipe. If you try it, let me know how it goes. Thanks!!

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