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These protein zucchini muffins are perfectly sweet, moist, and have more protein than traditional zucchini muffins. They’re made with simple, wholesome ingredients that you and your whole family will love.

Healthy Protein Zucchini Muffins
Whether you enjoy them for an easy breakfast or a quick snack, there’s just nothing better than a good muffin (especially with chocolate chips). And if you love these zucchini muffins, you’ll love my Healthy Chocolate Zucchini Bread and Chocolate Veggie Muffins too! Here’s why you’ll love these:
- Wholesome ingredients. These tender muffins are made with whole grains, lots of zucchini, Greek yogurt and sweetened with natural honey.
- Packed with protein. Most muffin recipes are pretty low in protein. One of these muffins packs 7 grams of protein, making them a great healthy snack option or protein-packed addition to your breakfast.
- No squeezing required. The best part? This isn’t one of those recipes where you need to squeeze excess moisture out of the grated zucchini with a paper towel. Just shred it and toss it in the bowl.
- Summer favorite. Zucchini breads and muffins are a classic during the hot months. These muffins are a great way to use up extra zucchini during the summertime.
Ingredients
For full recipe instructions and complete list of ingredients, scroll down to the recipe card at the bottom of this page.
Wet ingredients
- Shredded zucchini: You’ll use two whole cups of zucchini for these.
- Greek yogurt: Plain Greek yogurt works best to keep these muffins moist.
- Honey: For the perfect amount of natural sweetness. Or maple syrup!
- Avocado oil: Any neutral oil will work, but I love the healthy fats and neutral flavor of avocado oil.
- Eggs: Two large eggs add even more protein and hold the muffins together.
- Vanilla extract: Just a splash of vanilla.
Dry Ingredients
- Whole wheat flour: I use white or golden wheat flour for a lighter flavor but classic whole wheat or all purpose flour work as well.
- Protein Powder: To boost the protein I recommend vanilla whey-based protein powder. Use your favorite protein powder.
- Cinnamon: This warm spice is a must for zucchini muffins.
- Mini chocolate chips: For the best chocolate chip distribution in muffins I like to use mini chips. Regular size will work too.
- Baking powder, baking soda & salt
Variations
- Go nuts. Add ½ cup of chopped walnuts or pecans to the batter.
- Carrot zucchini muffins. Use 1 cup of shredded carrots and 1 cup zucchini.
- Mix up the chips. Use white chocolate chips, dark chocolate chips or even cinnamon chips.
- Make ’em chocolate. Use chocolate protein powder and add ¼ cup of unsweetened cocoa powder for healthy chocolate zucchini muffins.
- Gluten-Free. Use gluten-free flour in place of whole wheat. I like Bob’s Red Mill 1 to 1 Baking Flour.
- Use oats. Use half whole wheat flour and have oat flour for a chocolate chip zucchini oat muffin.
How To Make Zucchini Protein Muffins
- Mix dry ingredients. Add all dry ingredients to a large bowl and whisk to combine.
- Mix wet ingredients. Whisk together wet ingredients. Stir zucchini in last.
- Combine ingredients. Add wet ingredients to dry and mix until just combine. Transfer batter evenly into a muffin tin with liners. Add extra chocolate chips to the top of the muffin if desired.
- Bake. Bake at 350 degrees for 18-20 minutes, until a toothpick inserted in a center muffin comes out just clean. Check muffins right at 17-18 minutes for doneness because they do brown quickly.
How to Store
Before storing, cool to room temperature on a wire rack. Store leftovers in an airtight container for 3-4 days. I recommend storing in the fridge for best freshness. To warm them up, microwave for 10-15 seconds or slice in half and toast in a pan with butter.
Jamie’s Tips
Tips for Success
- Use a fine grate. Choose one of the finer grates on your box grater so that the zucchini pieces aren’t too thick and they release enough moisture.
- Choose a protein powder you like. Baking with protein powder can be tricky, so make sure you choose one that you enjoy! I love the Clean Simple Eats vanilla flavor.
- Don’t overbake. These muffins brown quickly in the last few minutes, so I highly recommend starting to check them at 17 minutes for doneness to avoid over baking. They should be done between 18-20 minutes.
- Line your muffin pan. I highly recommend using muffin liners for the best results, otherwise you risk the muffins sticking.
More Healthy Muffin Recipes
If you’ve made and loved this Protein Zucchini Muffins or any other recipe on my blog, please leave a 🌟 star rating and comments below!
Protein Zucchini Muffins
Ingredients
Wet ingredients
- 2 cups zucchini, grated (fine grate)
- 1/4 cup plain Greek Yogurt
- 1/2 cup honey
- 1/4 cup avocado oil
- 2 large eggs
- 1 tsp vanilla extract
Dry ingredients
- 1 1/2 cups white whole wheat flour, or "golden wheat"
- 1/2 cup vanilla protein powder
- 1 tsp baking powder
- 1 tsp baking soda
- 2 tsp cinnamon
- 1/2 tsp salt
- 2/3 cup mini chocolate chips
Instructions
- Preheat oven to 350 degrees F. Prepare a 12-tin muffin pan with paper liners.
- Add all dry ingredients to a large bowl and whisk to combine.
- In a medium bowl whisk together wet ingredients then stir in zucchini until well combined.
- Add wet ingredients to dry ingredients and mix until just combined. Transfer batter evenly between muffin tins. Top with extra chocolate chips.
- Bake 18-20 minutes, until a toothpick inserted in a center muffin comes out just clean. Start checking around 17 minutes to avoid overbaking. Tops brown quickly.
Notes
Nutrition
Nutrition information is automatically calculated and should only be used as an estimate.