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Superhero Apple Zucchini Carrot Muffins

These are called Superhero Muffins for good reason. They’re loaded with fresh apples, zucchini, and carrots, plus your favorite add-ins. These are gluten-free, dairy-free, and sweetened only with honey. These muffins are everything your body needs and your taste buds want. 

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Apple Zucchini Carrot Muffins

It feels fitting to bake something with major Superhero status this week. We need some beast-mode muffins worthy of wearing capes.

I mean, Shalane Flanagan won her marathons by eating these Superhero Muffins. (And maybe 100+ mile training weeks, but we don’t need to talk about that.) We adapted these healthy muffins from her Run Fast Eat Slow cookbook. Eating these made us want to sprint laps around the track. Instead, we got our steps in by trekking into the kitchen repeatedly for more muffins. It’s almost the same thing. 😇

These Apple Zucchini Carrot Superhero Muffins are stacked with nutrients, ultra moist, and taste winningly delicious…

superhero muffins, healthy muffin recipe, gluten free muffins, carrot muffins, zucchini muffins, apple muffins

What Ingredients go into Superhero Muffins?

These muffs are everything your body needs and 100% of what your taste buds want. These gluten free muffins are loaded with all the good stuff, none of the bad, and they’re truly delicious.

The action heroes in these superhero muffins include:

  • almond meal, rolled oats, cinnamon, vanilla, and any add-ins you like.
  • The add-ins are where you get to be creative. Any combination of nuts, seeds, dried fruits, or even chocolate chips are wonderful. In this particular batch, I went with chopped pecans, raisins, and dark chocolate chips.
  • Of course, we’ve got plenty of freshly grated apples, zucchini, and carrots. The original recipe uses only zucchini and carrots, but I love adding grated apples to the mix.

Variations and Ingredient Substitutions 

  • If you’d like to keep the muffins dairy-free, use coconut oil instead of butter. You can even try half applesauce/half oil. That’s going to be my next batch, as I think it would add to the apple-y vibes while cutting down on cals. Although, these muffins are already quite healthy as is.
  • You can go nut-free by using roasted pumpkin seeds (pepitas) or sunflower seeds in lieu of nuts. Chia seeds would also be great nutritionally and texturally.
  • To ensure these remain gluten-free muffins, be sure your containers are labeled gluten-free for the almond meal and rolled oats.
  • The dark chocolate chips are fully optional but totally yummy. Feel free to stick with dried fruits, if you don’t want the chocolate chips. Unsweetened white or dark raisins both work really well in this recipe. Chopped dates would be amazing, too.
  • Lastly, I like using pure honey for the sweetener, as it has such a rich golden flavor. You can substitute with equal amounts of pure maple syrup if you like.

Tips for making the best superhero apple zucchini carrot muffins:

  • Measure the almond meal and rolled oats carefully, so your dry ingredient to liquid ratio is accurate.
  • Use toasted nuts and/or seeds rather than raw, as they taste much better and have better crunch when toasted.
  • I prefer to use the fine side of box grater for my carrots, zucchini, and apples, as the finer texture allows the veggies to blend into the batter easier. However, some people like the texture of the larger shredding holes.
  • Do not squeeze excess liquids from the grated veggies/fruits. Include the juices, as it will help provide moisture to the finished muffins.
  • Be sure to use a rubber spatula to gently fold dry ingredients with wet ingredients to form the batter; don’t over mix, as that typically results in a tougher texture.
  • Muffin cups should be filled to the brim before baking; they won’t rise as much as other muffins do.
  • The ultimate tip: be sure to check muffins 2-3 minutes before bake time is done, just to ensure they’re not becoming over-baked. Over-baked goodies just aren’t as good.

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Why You’ll Love these Superhero Muffins

  • They make you run like Shalane.
  • Not really to the above, but you might feel like a champ while eating these muffins.
  • These muffins are loaded to the max with nutrients, protein, fiber, antioxidants, etc.
  • Simultaneously, these superhero muffins taste spectacular.
  • Our gluten-free, dairy-free, and even refined-sugar-free friends can enjoy these muffins right along with us.
  • These muffins are always a hit with family and friends.
  • These treats are awesome fuel to satisfy those midday hunger cravings.
  • My picky teens inhale these muffins. ‘Nuff said.

Did you make this?

Please give us a rating and comment below. We love hearing from you!

Closed up of muffins with chocolate chunk

Superhero Apple Zucchini Carrot Muffins

4.86 from 14 ratings
These are called Superhero Muffins for good reason. They’re loaded with fresh apples, zucchini, and carrots, plus a dose of chocolate chips if you’re so inclined. These are gluten-free, dairy-free, and sweetened only with honey. These muffins are everything your body needs and your taste buds want. 
Prep Time: 30 minutes
Cook Time: 25 minutes
Servings: 12
Author: Amy Dong


  • 2 cups almond meal
  • 1 cup gluten-free old-fashioned rolled oats
  • ½ cup chopped, toasted pecans (or other nuts/seeds of your choice)
  • ½ cup raisins or other dried fruit
  • ½ cup dark or semi-sweet chocolate chips, optional
  • 2 teaspoons ground cinnamon
  • ½ teaspoon ground nutmeg
  • 1 teaspoon baking soda
  • ½ teaspoon fine table salt
  • 3 large eggs, lightly beaten
  • ½ cup grated zucchini, no need to peel
  • ½ cup peeled, grated carrot
  • 1 cup peeled, shredded apple
  • 6 tablespoons melted coconut oil, or butter
  • ½ cup pure honey
  • 2 teaspoon vanilla
  • paper muffin liners


  • Arrange a rack in the center of the oven and preheat the oven to 350°F. Line a 12-cup standard muffin tin with paper muffin cups.
  • In a large bowl, combine the almond meal, oats, pecans, raisins, chocolate chips, cinnamon, nutmeg, baking soda, and salt. Stir to incorporate well. In a separate large bowl, use a hand whisk to stir together the eggs, zucchini, carrot, apple, coconut oil (or butter,) honey, and vanilla. Use a rubber spatula to gently fold the dry ingredients into the wet ingredients, folding until just combined; do not over-mix batter.
  • Divide the batter evenly into the muffin cups, filling each to the brim. Bake about 25 minutes, or just until the muffins are golden on top and a toothpick inserted in the center of a muffin comes out with a few tender crumbs attached. Start watching a couple minutes before bake time is up, to ensure muffins are not over-baked.
  • Let muffins come to almost room temp before removing from muffin tin. Muffins are best served the day they’re made, but can be kept in airtight container at room temp for 2 days.


**Using butter and semi-sweet chocolate chips are totally optional. To keep these muffins dairy free, use coconut oil. To keep them refined-sugar free, stick with nuts, seeds, or unsweetened dried fruits for the add-ins. ** Baked muffins can be wrapped airtight the day they’re made and frozen for breakfast on-the-go.

Nutrition (per serving)

Calories: 265kcal | Carbohydrates: 24.4g | Protein: 6.8g | Fat: 15.4g | Saturated Fat: 6.8g | Cholesterol: 46.5mg | Sodium: 224.8mg | Fiber: 4.3g | Sugar: 14.1g
Course: Breakfast
Cuisine: American
Method: Oven

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4.86 from 14 votes (5 ratings without comment)

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Recipe Rating


    • Brenna
    • 5 stars

    I’m on a very restricted diet for health reasons and these are a GODSEND. How would you convert them to a cake. It’s easier for me to pour the whole thing into a cake pan and skip the cupcake papers.

    • Haley
    • 5 stars

    I had my doubts, but these actually are so amazing. I made a double batch and I am so happy I did. I immediately ate two. My husband is going to be obsessed with them. Yes finally a breakfast muffin we can make regularly!

    • Megan
    • 5 stars

    I absolutely love these! They are guilt free and a great post workout snack. I make a batch and freeze them so I can pop one out whenever I want. I did sub maple syrup for the honey and use Lilly’s brand stevia sweetened chocolate chips. Thank you for sharing!

    • Bindu Thomas

    This looks so delicious and I will definitely try this one. Thanks for sharing.

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