Zucchini Flaxseed Muffins {Freezer Meal}

I’ve made these Zucchini Flaxseed 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.

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

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.

#1 – Why Eat Flaxseed?

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 listed on www.whfoods.org, which explains them in much further detail:

  • 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

#2 – 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 Flaxseed 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.
  • 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.
  • Make a double batch of these and freeze them for healthy and quick breakfasts and lunches. To warm up, microwave for 30 seconds and check on them. Then turn and microwave 15 seconds more at a time until warmed through.

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.

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

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.

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 this 9×13 Glass Baking Dish with a BPA-free TrueFit Lid* from MightyNest (pictured below). If you’re going to buy one freezer storage container, make it this one. You’ll find that a large amount of recipes you make will call for a 9×13 size pan. You’ll realize that having a lid to one of these dishes is a godsend.*affiliate link

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.

Zucchini Flaxseed Muffins
Prep time
Cook time
Total time
Serves: 24 muffins
  • 1 cup whole wheat flour (I use the white variety of whole wheat flour)
  • ½ 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
  • ½ 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 ¼ 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.
Nutrition Information
Serving size: 1 muffin

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 favorites like…

Pumpkin Chocolate Chip Muffins

healthy pumpkin muffin

Chocolate Banana Muffins

Whole Wheat Chocolate Pumpkin Banana Muffins

Pumpkin Muffins with Crumble Topping


  1. 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 🙂

  2. Rachel says

    Thanks for sharing this recipe! Looks yummy and healthy–my fav.

  3. Kathy says

    The muffins look yummy but what’s really great about this entry is the adorable twinkle in Hannah’s eyes.

  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.

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  6. 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 !

  7. 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!

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