Protein Zucchini Muffins

Jump to Recipe Print Recipe

These Protein Zucchini Muffins are soft, fluffy, and packed with warm cinnamon flavor, melty chocolate chips, and a boost of protein in every bite. They’re an easy make-ahead breakfast or snack that sneaks in veggies while tasting just like classic zucchini bread.

protein zucchini muffins in liners on white plate.

The Most Glorious Muffins

I grew up on my grandma’s zucchini bread recipe (yes, this is the same grandma who made the Simple Banana Sheet Cake recipe!). So when I received some zucchini from her garden this year, I knew I had to make a zucchini protein muffin version of her chocolate zucchini bread or as close to it as I could get!

These Protein Zucchini Muffins have all the nostalgic flavors of traditional zucchini bread, but with extra protein to help keep you full longer. The zucchini keeps every muffin incredibly moist without making them taste “veggie-forward,” while the cinnamon and chocolate chips make each bite feel like a treat. They’re perfect for meal prep because they freeze beautifully and are easy to grab on busy mornings. Whether you’re trying to use up garden zucchini or simply looking for a satisfying breakfast or snack for the kiddos, a batch of these muffins checks every box.

Recipe Inspo

Protein muffins do really well on APOP – and for a good reason. They’re well tested, we have a variety of options (Chocolate Banana Protein Muffins to Pumpkin Protein Muffins (use a whole can of pumpkin!!), and more fruity like: Cherry Pistachio Muffins or Blueberry Protein Muffins). If you love muffins, I have the recipes for you!

Recipe Ingredients

ingredients for protein zucchini muffins in separate bowls.

Brown Sugar – For sweetness! Adds more moisture than white sugar.
Zucchini – We’ll use 1 medium zucchini, moisture NOT removed. If you have more than 1 ¼ cup of shredded zucchini, you can add it but remove the moisture from it so it doesn’t affect the integrity of the muffins.
Yogurt– I used vanilla Greek yogurt. It adds the perfect richness.
Flour – I used all purpose flour and have not tried alternatives so substitute with caution.
Collagen Powder – I like the unflavored from Vital Proteins. It is so easy to use while baking.
Cinnamon & Vanilla – For bakery style flavors!
Mini chocolate chips – A must! The more the better;)

See the recipe card below for a full list of ingredients and measurements.

Substitutions and Variations

I love adding chopped walnuts or pecans into the batter or sprinkling them on top before baking for a little crunch.
Swap the mini chocolate chips for dark chocolate chips, white chocolate chips, or raisins.
Use plain Greek yogurt instead of vanilla Greek yogurt if that’s what you have on hand.
Add ½ teaspoon of nutmeg or pumpkin pie spice for even more cozy flavor.
Stir in a tablespoon of ground flaxseed or chia seeds for an extra nutrition boost.

How to Make This Recipe

1. Preheat the oven to 350°F and line a muffin tray with tulip muffin liners. Spray with cooking spray, set aside.

ingredients for protein zucchini muffins in large mixing bowl.

2. In a large mixing bowl, combine brown sugar, shredded zucchini, greek yogurt, eggs, and vanilla extract. Use an electric hand mixer to mix until combined.

3. Pour in the flour, collagen, ground cinnamon, baking powder, and salt. Beat again until combined.

protein zucchini muffin batter in large mixing bowl with chocolate chips added on top.

4. Gradually pour in the oil while mixing the batter. Once thoroughly combined, pour in the mini chocolate chips and mix.

protein zucchini muffin batter in liners in gray muffin tin before baking.

5. Use a cookie scooper to fill the muffins almost to the top of their liners to make 12 even sized muffins. Sprinkle more mini chocolate chips on top of the muffins before baking.

6. Bake for 25-28 minutes or until the centers are firm, a toothpick comes out clean and the internal temperature of the muffins is 200°F.

7. Remove the muffins from the tin, allow to cool before storing.

PRO TIPS

A trick I like is to use a meat thermometer to tell you the doneness of the muffins. Once the muffins reach 200°F, they are finished cooking but not to the point that they are too dry inside!
For all of my protein recipes, I use Tulip Muffin Liners! This is because they help the muffins bake up nice and tall, prevent sticking, and make them look bakery-worthy every single time. They’re one of my favorite little baking hacks for getting consistent results.

Recipe FAQs

How do we store them?

Store the zucchini chocolate chip muffin in an airtight container on the counter for up to 3 days or in the refrigerator for up to 1 week. For longer storage, freeze them in a freezer-safe bag or container for up to 3 months. Let them thaw at room temperature or warm one in the microwave for 20–30 seconds before enjoying.

Do I need to squeeze the moisture out of the zucchini?

No! For this recipe, leave the moisture in the zucchini if you’re using up to 1¼ cups. That natural moisture helps create soft, tender muffins. If you end up with more than 1¼ cups of shredded zucchini, squeeze out some of the excess liquid with paper towels before adding the extra amount to the batter.

Can I use protein powder instead of collagen?

Collagen mixes seamlessly into the batter without affecting the texture, which is why it’s my preferred option. If you’d like to substitute a protein powder, choose a vanilla protein powder you enjoy baking with, but keep in mind that whey and plant-based powders absorb moisture differently and may result in a slightly denser muffin. You may need to add a splash of milk if the batter seems too thick.

Serving suggestions

These Protein Zucchini Muffins are perfect as a pre-workout snack, an easy breakfast on busy mornings, or tucked into lunchboxes for an afternoon pick-me-up.

Pair one with a bowl of Greek yogurt and fresh berries for a more filling breakfast, or enjoy it alongside scrambled eggs for extra protein. They’re also delicious with a cup of coffee or a homemade latte during slow weekend mornings. Or meal prep along side some Banana Peanut Butter Overnight Oats for grab-and-go breakfasts all week long.