These flax muffins are my new obsession! Full of feel-good ingredients like whole wheat flour, ground flax + Greek yogurt, but they are delightfully moist + tender thanks to the addition of grated zucchini and juicy blueberries. Mixed up in one mixing bowl + baking up in just 20 minutes, these muffins make such a hearty breakfast or get-me-through-until-dinner afternoon snack!

Several blueberry muffins in paper liners sitting on a countertop surrounded by loose blueberries.

I know what you’re thinking…flax muffins? As soon as flax (or bran!) come into the mix, people tend to say “no thanks!” But I swear that these are not dense hockey pucks you might imagining right now!

Actually, quite the opposite! Sure, these flax muffins are full of hearty, good-for-you ingredients like whole wheat flour and ground flax (obviously), but the added grated zucchini, Greek yogurt, and applesauce add all kinds of moisture, making these muffins moist, tender and fluffy to boot. And then I’ve naturally sweetened these muffins with a little maple syrup (or honey) and studded them with poppin’ juicy blueberries for that perfect morning muffin vibe.

Not only are they nutrient-dense, but they also clock in with a whopping 6 grams of fiber + 7 grams of protein per muffin…with zero protein powders required! And they are mixed up in one bowl + done baking in just 20 minutes…so add these blueberry zucchini muffins to your meal prep line up, since they don’t make a lot of dishes or take a ton of time.

All the ingredients for Zucchini Blueberry Flax Muffins sitting together before baking.
Ingredients: zucchini, eggs, unsweetened applesauce, avocado oil, maple syrup, vanilla extract, plain Greek yogurt, baking powder, baking soda, kosher salt, ground cinnamon, ground nutmeg, ground flaxseed, whole wheat flour, blueberries

How to make these flax muffins

If you are a visual person, here is a picture guide for how the recipe should look at each step. Be sure to grab the exact measurements for the ingredients by scrolling down to the recipe card below.

Zucchini being grated with a hand grater on a cutting board. Cutting board is sitting on a countertop and is surrounded by remaining ingredients for the muffins.
Grate the zucchini.
Wet ingredients for muffin recipe are in a glass bowl sitting on a countertop. Bowl is surrounded by a whisk and cracked eggshells.
In a large bowl, add the grated zucchini, eggs, applesauce, oil, maple syrup, vanilla, and yogurt.
Wet ingredients for muffins being mixed together with a whisk in a glass bowl. Bowl is sitting on a countertop and is surrounded by cracked eggshells.
Whisk until combined.
Baking powder, baking soda, salt, and cinnamon being whisked into wet ingredients for muffins in a glass bowl. Bowl is sitting on a countertop and is surrounded by cracked eggshells.
Whisk in the baking powder, baking soda, salt, and cinnamon.
Ground flax and flour sitting on top of wet ingredients for muffins in a glass bowl. Bowl is sitting on a countertop and is surrounded by cracked eggshells.
Add the ground flax and flour.
Dry ingredients are being mixed into wet ingredients for muffin recipe using a spatula. Ingredients are being mixed in a glass bowl sitting on a countertop. Bowl is surrounded by cracked eggshells.
Mix together with a large spoon or rubber spatula until all the ingredients are just combined. Do not over mix. Over mixing can lead to dense muffins and we are going for fluffy.
Blueberries being folded into muffin batter in a glass bowl with a spatula. Bowl is sitting on a countertop.
Fold in the blueberries.
Muffin batter being portioned out with a cookie scoop into a paper lined muffin tin. Bowl of muffin batter is sitting on a countertop.
Heat the oven to 375℉. Line a standard muffin tin with paper liners or grease with oil spray.
A muffin tin filled with blueberry muffins in muffin liners. The muffin tin is sitting on a countertop.
Bake until the muffins have an internal temperature of 200℉ and are lightly golden brown, about 20-22 minutes.
Several baked blueberry muffins in paper liners sitting on parchment paper on a cooling rack. Muffins are surrounded by a bowl of blueberries, a bowl of flax seeds, a napkin, and loose blueberries strewn about on the counter.
Let the muffins cool in pan for about 10 minutes before enjoying warm or allow them to cool fully then store in an airtight container in the fridge for 4 to 5 days or well wrapped in the freezer for 1 month.

Recipe testing notes from Taesha

  • Replace the blueberries with raspberries.
  • You can use frozen blueberries, however they will turn your muffins a bit of a purple color!
  • Swap the maple syrup for honey, if you prefer.
  • Make them as mini muffins, baking for about 13-15 minutes.
  • If you have a kitchen thermometer, cook until the muffins have an internal temperature of 200℉. This will ensure they are cooked through, but not overcooked.
  • Replace the applesauce with mashed ripe bananas.

Other veggie-loaded muffin recipes to bake up!

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An unwrapped blueberry muffin with a bite taken out of it. Muffin is sitting on a countertop surrounded by loose blueberries and a couple more muffins slightly out of frame.
4.60 from 5 votes

Feel-Good Zucchini Blueberry Flax Muffins

Yield: 12 muffins
Prep Time: 15 minutes
Cook Time: 20 minutes
Cuisine: American
Course: Breakfast, muffin
These flax muffins are my new obsession! Full of feel-good ingredients like whole wheat flour, ground flax + Greek yogurt, but they are delightfully moist + tender thanks to the addition of grated zucchini and juicy blueberries. Mixed up in one mixing bowl + baking up in just 20 minutes, these muffins make such a hearty breakfast or get-me-through-until-dinner afternoon snack!

Ingredients
 

  • 1 cup grated zucchini , do not squeeze out the moisture
  • 2 large eggs
  • cup unsweetened applesauce
  • ½ cup plain Greek yogurt
  • cup maple syrup
  • cup avocado oil
  • 2 teaspoons vanilla extract
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon kosher salt
  • 1 teaspoon ground cinnamon
  • ¼ teaspoon ground nutmeg
  • 1 cup ground flaxseed
  • cup whole wheat flour
  • cup blueberries, + extras for topping

Instructions
 

  • Heat the oven to 375℉. Line a standard muffin tin with paper liners or grease with oil spray.
  • In a large bowl, whisk the grated zucchini, eggs, applesauce, oil, maple syrup, vanilla, and yogurt until combined.
  • Whisk in the baking powder, baking soda, salt, nutmeg, and cinnamon.
  • Add the ground flax and flour and then mix with a large spoon or rubber spatula until all the ingredients are just combined. Do not over mix. Over mixing can lead to dense muffins and we are going for fluffy.
    Fold in the blueberries.
  • Scoop the batter into each muffin cup, filling almost to the top. Top the muffins with extra blueberries, if desired.
  •  Bake until the muffins have an internal temperature of 200℉ and are lightly golden brown, about 20-22 minutes.
  • Let the muffins cool in pan for about 10 minutes before enjoying warm or allow them to cool fully then store in an airtight container in the fridge for 4 to 5 days or well wrapped in the freezer for 1 month.
Serving: 1muffin, Calories: 234kcal, Carbohydrates: 24g, Protein: 7g, Fat: 13g, Saturated Fat: 2g, Polyunsaturated Fat: 5g, Monounsaturated Fat: 6g, Trans Fat: 0.003g, Cholesterol: 32mg, Sodium: 200mg, Potassium: 240mg, Fiber: 6g, Sugar: 8g, Vitamin A: 81IU, Vitamin C: 3mg, Calcium: 89mg, Iron: 2mg