Zucchini Muffins with Flaxseed

By Rachel Tiemeyer
May 11, 2021
Healthy zucchini muffins

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I’ve made these Zucchini Muffins more times than I can count. Not only are they moist and totally yummy, but they are a great way to include some sneaky nutrition into a kid-favorite. I almost always make two batches, freeze one for later, and then ration them out for breakfast and snacks.

Now, before we get to the Zucchini Muffins recipe, let’s look at some health motivation and thrifty tips that I think will motivate you to make these. Shall we?

Healthy Zucchini Muffins

Why is there Flaxseed in the Zucchini Muffin Recipe?

This is important to answer, because once you do I think you’ll be highly motivated to find ways to ingest it (i.e. by making the muffin recipe below).  Here are just a few of the health benefits:

  • helps reduce inflammation (which can be a significant factor in conditions such as migraine headaches, rheumatoid arthritis, diabetes, asthma, inflammatory bowel disease, etc.
  • protects bone health
  • protects against heart disease, cancer (especially colon, breast, and prostate), and diabetes
  • helps prevent and control high blood pressure
  • rich in beneficial fiber
  • fends off dry eyes

Read more about why flaxseed is good for you here.

Time & Food Saving Ideas

This is one of those recipes that is very forgiving and a great way to use up old or frozen fruits and vegetables. Check out some of these ideas I’ve done in the past to save food and time when making these Zucchini Muffins.

  • Grate zucchini or summer squash using a box grater and freeze it in a freezer bag until you’re ready to use it. To defrost, leave on the counter, in the fridge (with a plate under it), or run under warm water while in the freezer bag. Squeeze out some of the water from the thawed zucchini by twisting it in a kitchen towel over the sink. Here is a whole post about how to freeze zucchini, if you want to read more.
  • Use the leftover pulp in your juicer after juicing! I have been freezing my pulp to use when I’m ready to make muffins like these. It worked beautifully in place of the grated carrots in the recipe. My pulp consisted of carrots, apples, grapes, and spinach! It all went in the blender and no one ever knew the difference. Amazing what you can put in muffins!
  • Throw old bananas in the fridge (lasts about a week longer) or the freezer (lasts about a month or so longer) and use in this recipe when ready. Here is more info on how to freeze bananas.
  • Make a double batch of these and freeze them for healthy and quick breakfasts and lunches. To warm up, microwave in 30 second increments until warmed through.
Overhead shot of zucchini muffins in a casserole dish ready to freeze

Now that you’re motivated to kick your health up a notch and save some old food from going bad, let’s get to making some delicious Zucchini Flaxseed Muffins.  Enjoy!

Zucchini muffins in a muffin tin

How to Freeze Zucchini Muffins

If you decide to make these in bulk and freeze them, here are the two great ways to store or freeze muffins

I personally like using an this Glass Baking Dish with a BPA-free TrueFit Lid. If you’re going to buy one freezer storage container, make it this one. Polly and I are stocked up on these dishes and use them for most of our freezer meals.

These freezable Zucchini Flaxseed Muffins are not only moist and totally yummy, but they are a great way to include some sneaky nutrition into a kid-favorite.

Hey, guess what? If you like this healthy muffin recipe, Polly and I have loads more healthy baked goodies in our Recipe Index.  Check out a few of our freezable favorites like…

Banana Pumpkin Muffins

Chocolate Banana Muffins

Blueberry Power Muffins

Whole Wheat Chocolate Chip Zucchini Bread


Zucchini Muffins with Flaxseed

  • Author: Thriving Home
  • Prep Time: 10 minutes
  • Cook Time: 15 minutes
  • Total Time: 25 minutes
  • Yield: 24 muffins 1x
  • Category: Bread
  • Method: Baked
  • Cuisine: American


These zucchini flaxseed muffins are a great way to include some sneaky nutrition into a kid-favorite treat. Whole wheat flour, ground flaxseeds, carrots, and bananas are just a few of the key ingredients in these fantastic muffins.


  • 1 cup whole wheat flour (I use the white variety of whole wheat flour)
  • 1/2 cup unbleached white flour
  • ¾ cup ground flaxseed (or you can sub dried coconut)
  • ¾ cup oats (quick or rolled works fine)
  • 1 cup turbinado sugar or brown sugar
  • 2 teaspoons baking soda
  • 1 teaspoon baking powder
  • ½ teaspoon salt
  • 2 teaspoons cinnamon
  • ¾ cup milk
  • 2 eggs
  • 1 teaspoon vanilla
  • 1 cup grated zucchini or summer squash
  • 1/2 cup grated carrots
  • 1 ripe banana, smashed
  • 1 c nuts, chopped (optional)


  1. In a large bowl, mix together flours, flaxseed, oats, sugar, baking soda, baking powder, salt, and cinnamon.
  2. In a separate bowl, blend together the following wet ingredients: milk, eggs, vanilla, grated zucchini, grated carrots, banana. (Note: I often use my blender for this step, as I have found it makes all the veggies “disappear” into the batter for picky eaters.)
  3. Pour liquid ingredients into dry ingredients and stir until ingredients are just moistened. Stir in nuts, if wanted. Do not over mix.
  4. Fill greased muffin tins about ¾ of the way full (about 1/4 cup of batter per muffin hole).
  5. Bake at 350 degrees for 13-15 minutes, until a toothpick inserted in the middle comes out clean.


Freezer Meal Instructions:

To Freeze: Fully bake and cool muffins. Store in a single layer in a gallon-sized freezer bag or container.

To Prepare: Let thaw on the counter. Or wrap a frozen muffin in a moist paper towel and microwave in 30 seconds increments until warmed through.


  • Serving Size: 1 muffin

Want More Make Ahead Breakfast Ideas?

Be sure to check out these 3 Make Ahead Breakfasts that we know you will love!

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17 replies
  1. Carley says:

    I want to make these but I don’t have carrots. Any ideas on how I can substitute? Thanks for your wonderful recipes! I especially love your new freezer cookbook! I use it often. ?

  2. Dorothy says:

    I love the sound of your newest recipe for zucchini and fax seed muffins but they call for banana, I HATE banana’s but I am also allergic to them, can I replace them with something else, like more carrots and zucchini or raisins

    • Rachel says:

      Hi Dorothy, you can certainly replace banana with other veggies or fruit purees like applesauce, finely shredded zucchini, or pumpkin puree. I hope that helps!

  3. Rei says:

    I had confused two different recipes, duh! Sorry ! I was thinking of A scone recipe that needs to be baked at 400. Love this recipe, thank you !

  4. Rei says:

    I love this recipe, but I really think you made a mistake about the baking temperature. I recall the previous time I saw you post this recipe, it said you were supposed to bake the muffins at 400°. I’ve tried baking on the 350 and they don’t come out at all.

    • Rachel says:

      Did 400 degrees work for you? I went back and checked the original recipe and it says 350. I made them just the other day and that temperature worked. I suppose altitude and/or just oven temperature differences could account for some of the issue. I don’t bake any muffins at 400 where I live, though. They always burn.

  5. Rebecca says:

    These look delicious! I’ll have to try them. I’m in need of some sneaky ways to get my kiddo to eat his vegetables 🙂