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Protein Zucchini Muffins Recipe

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We know that finding perfect balance between clean ingredients, satisfying flavor, and high-performance nutrition can be challenging—especially when it comes to baked goods. That’s why for any fitness enthusiast these Protein Zucchini Muffins are a must have recipe. Packed with lean protein, naturally sweetened, and loaded with fiber-rich zucchini, they work great as a pre-workout bite, a midday snack, or even part of your meal prep routine.

We know you aren’t a fan of dry and chalky protein muffins. Protein Zucchini Muffins are moist, tender, and deliciously spiced. You’ll get a protein boost without compromising taste or clean-eating principles.

Macros That Make Sense

Every ingredient in these muffins serves a purpose. While remaining virtually flavorless zucchini adds moisture and fiber. Oat flour and protein powder create a nutrient-dense base that sustains energy and fuels your muscles. You also get high-quality protein and healthy fats from Greek yogurt and eggs, while honey or maple syrup keeps the muffins sweet—but not sugary.

These muffins are a smart choice for anyone training hard or watching macros because unlike traditional bakery muffins that spike your blood sugar, these offer slow-burning carbs and a higher protein profile.

Ingredients (Makes 12 Muffins)

  • 1 cup finely grated zucchini (squeeze out excess moisture)
  • 2 large eggs
  • 1/2 cup plain Greek yogurt (non-fat or low-fat)
  • 1/4 cup unsweetened applesauce
  • 1/4 cup honey or pure maple syrup
  • 1 teaspoon vanilla extract
  • 1 cup oat flour (blend rolled oats if needed)
  • 1/2 cup vanilla protein powder (whey or plant-based)
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • 1 teaspoon ground cinnamon
  • 1/4 teaspoon ground nutmeg (optional)
  • 1/4 teaspoon sea salt
  • Optional: 1/4 cup chopped walnuts or dark chocolate chips

Instructions

1. Preheat the Oven

Begin by setting your oven to 350°F (175°C). While it heats, line a standard 12-cup muffin tin with paper liners or lightly spray it with non-stick cooking spray. You want to prevent sticking while keeping the fat content in check.

2. Prepare the Zucchini

Use a fine grater to shred the zucchini. After measuring out one packed cup, place it in a clean kitchen towel or cheesecloth and squeeze out as much water as possible. Moisture content can vary, and too much will make the muffins soggy, so don’t skip this step.

3. Combine Wet Ingredients

In a large mixing bowl, whisk together the eggs, Greek yogurt, applesauce, honey (or maple syrup), and vanilla extract. Stir until the mixture turns smooth and creamy.

4. Add the Zucchini

Fold the shredded zucchini into the wet mixture. Stir until evenly incorporated. This step adds fiber, moisture, and volume to the batter without overwhelming the flavor.

5. Mix Dry Ingredients

In a separate bowl, combine the oat flour, protein powder, baking soda, baking powder, cinnamon, nutmeg (if using), and salt. Stir well to distribute all the leavening agents and spices evenly.

6. Combine Wet and Dry

Slowly add the dry mixture to the wet bowl. Use a silicone spatula or wooden spoon to stir the batter gently, being careful not to overmix. Once no dry streaks remain, stop stirring. If you’re adding mix-ins like walnuts or dark chocolate chips, fold them in now.

7. Fill the Muffin Tin

Scoop the batter into the prepared muffin tin, filling each cup about 3/4 full. Use a spoon or cookie scoop to make the process quick and even.

8. Bake

Place the muffin tin in the center of your preheated oven. Bake for 18 to 22 minutes, or until a toothpick inserted into the center comes out clean. The tops should look golden and slightly domed.

9. Cool and Store

After baking, let the muffins cool in the pan for 5 minutes. Then transfer them to a wire rack to cool completely. Once cooled, store in an airtight container at room temperature for up to 3 days or refrigerate for up to a week. You can also freeze them for up to 2 months.

Nutrition Facts (Per Muffin)

Nutrient Amount
Calories 145 kcal
Protein 10g
Carbohydrates 14g
Dietary Fiber 2g
Total Sugars 6g
Total Fat 5g
Saturated Fat 1g
Cholesterol 35mg
Sodium 160mg

Nutrition may vary slightly depending on protein powder and mix-ins used.

Muffin Hacks for Your Goals

  • Post-Workout Snack: If you want balanced recovery snack, just pair one muffin with a banana or hard-boiled egg
  • Boost Calories: If you need more fuel for bulking or intense training phases, add a tablespoon of almond butter or peanut butter
  • Lower the Carbs: Use almond flour in place of oat flour for a lower-carb version, but expect a slightly denser texture.
  • Vegan Option: Replace the eggs with flax eggs, Greek yogurt with coconut yogurt, and use plant-based protein powder.

One Last Thing Before You Bake

With these Protein Zucchini Muffins clean eating is easy, especially for active people who want food that works as hard as they do. You’ll enjoy every bite while knowing you’re fueling your body with purpose.

Protein Zucchini Muffins

Perfectly sweet, moist and tender zucchini muffins with more protein than traditional zucchini muffins.
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Servings 12
Calories 220 kcal

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

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,

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