Best Ever Protein Zucchini Muffins That Taste Incredible

These sweet, moist zucchini muffins are the perfect healthy sweet treat! They’re packed with more protein than a traditional muffin, plus they’re gluten free and low carb. With a delicious texture and just the right amount of sweetness, these muffins are the perfect treat you can feel good about enjoying.

Since I cut out all refined sugar from my diet, I’m always experimenting with healthy sweet treats that actually satisfy a craving.

This zucchini muffin recipe has evolved over time, and I think it’s finally perfect enough to share!

They’re moist, sweet, gluten free, made with no refined sugar, and low in carbs—everything you could want in a sweet and delicious treat.

And as summer winds down and we’re harvesting lots of zucchini, this is the perfect recipe for using up some of those zucchini you may be getting a little tired of!

The muffins come together quickly and freeze beautifully, too.

Woman holds a moist protein zucchini muffin with chocolate chips.

So grab that zucchini and start making my protein zucchini muffins today.

You’ll have a healthy sweet treat ready to enjoy without the guilt!

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Why You’ll Love These Protein Zucchini Muffins

If you’re a fan of moist zucchini bread with chocolate chips, then you are going to LOVE these healthy zucchini muffins!

They have all the delicious flavor and texture of a moist slice of zucchini bread, without all the carbs, and they’re packed with protein.

It’s a win-win!

They’re the perfect treat when you’re craving something sweet, and I especially love that there’s no refined sugar in this recipe.

A plate of moist protein zucchini muffins with chocolate chips.

About two years ago, I discovered that refined sugar was causing my migraines, so I decided to give it up completely.

That can be challenging when you realize how much refined sugar is hiding in processed foods, so these days I make most of our meals and treats from scratch.

And honestly, recipes like these makes it so much easier!

So, are you ready to give these muffins a try?

  • Moist and delicious
  • Naturally sweet
  • High in protein
  • No refined sugar
  • Low carb
  • Gluten free
  • Easy to make
  • Freezer friendly
  • A satisfying sweet treat

What Makes These Muffins Different?

So, what makes these protein zucchini muffins different from a traditional zucchini muffin?

There are a few little secrets that make a big difference!

First, I added protein powder, which not only increases the protein but also helps create a moist, tender texture.

Another unexpected ingredient is tahini.

It adds a subtle nutty flavor that you can’t quite put your finger on, but it makes these muffins taste even better.

And, of course, there’s plenty of grated zucchini, which is the real star when it comes to keeping these muffins incredibly soft and moist without overpowering their delicious zucchini-bread flavor.

Woman holds half a protein zucchini muffin with chocolate chips over a charcuterie board with protein muffins.

Here are a few things that make these muffins special:

  1. Protein-packed: Protein powder gives these muffins more protein than a traditional zucchini muffin while also helping improve their texture.
  2. Super moist: While the protein powder adds moisture, it’s the grated zucchini that really makes these muffins so soft and moist.
  3. Naturally sweet: Instead of refined sugar, we use organic monk fruit. It’s an easy swap, and honestly, you can’t taste the difference!
  4. Lower in carbs: Traditional white flour is replaced with a combination of almond flour and coconut flour, keeping these muffins lower in carbs while still giving them a delicious texture.
  5. A little tahini magic: Tahini may seem like an unusual muffin ingredient, but its subtle flavor adds just the right amount of richness and makes these muffins even more delicious.

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Ingredients You’ll Need

The ingredient list for these protein zucchini muffins is pretty simple, and you may already have most of it in your pantry.

A few ingredients, like the protein powder, tahini, and almond and coconut flour, are what give these muffins their protein-packed, low-carb texture.

Here’s everything you’ll need to get started:

Dry Ingredients

  • Super fine almond flour – creates a tender, moist texture while keeping the muffins lower in carbs.
  • Coconut flour – helps absorb moisture and gives the muffins structure.
  • Vanilla protein powder – adds a boost of protein and contributes to the soft, moist texture. I prefer Just Ingredients protein powder because of the clean ingredients.
  • Baking soda – helps the muffins rise.
  • Ground cinnamon – adds that warm, cozy zucchini-bread flavor.
  • Salt – enhances all the other flavors.
  • Monk fruit – our refined-sugar-free sweetener.

Wet Ingredients

  • 4 large eggs, room temperature
  • Tahini – adds a subtle nutty richness and extra depth of flavor.
  • Milk or almond milk – adds moisture to the batter.
  • Vanilla extract – enhances the sweetness and overall flavor.
  • Melted coconut oil, cooled – adds moisture and richness.
  • Finely shredded zucchini – the secret to these muffins’ incredibly moist texture.
  • Sugar-free chocolate chips (optional) – because a little chocolate makes these zucchini muffins extra delicious!

You’ll Also Need


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How to Make Protein Zucchini Muffins

These muffins come together quickly and easily, so let’s get baking! Start by preheating your oven to 350°F.

1. Combine the dry ingredients

Whisk together the dry ingredients.


Place the superfine almond flour, coconut flour, vanilla protein powder, baking soda, cinnamon, salt, and monk fruit in a large mixing bowl.

Whisk everything together until well combined.

2. Mix the wet ingredients

Whisk together the wet ingredients.


In a separate medium mixing bowl, add the eggs, tahini, milk or almond milk, vanilla, and cooled melted coconut oil.

Whisk until everything is well combined.

3. Combine wet and dry ingredients

Zucchini batter after the wet and dry ingredients are combined in a stainless steel bowl.

Then place all of the wet ingredients except for the zucchini in a medium mixing bowl and whisk until well combined.

This will form a stiff batter.

4. Add the zucchini

Add the finely shredded zucchini along with any liquid released while shredding to the batter.

Stir until the zucchini is evenly incorporated.

5. Fill muffin pan

A muffin tin lined with paper liners and filled with protein zucchini muffin batter and sprinkled with sugar-free chocolate chips.

Place paper liners in your muffin pans and divide the batter evenly between 22 cups, filling each one about ¾ full.

6. Bake

Bake at 350°F for 20–24 minutes.

I find that 22 minutes is perfect in my oven, but every oven is a little different.

To check for doneness, insert a toothpick into the center of a muffin.

It should come out clean or with just a few moist crumbs.

Baking tip

Be careful not to overbake these muffins!

They can become dry if they stay in the oven too long.

Keep a close eye on them toward the end of the baking time.

Don’t Forget the Chocolate Chips!

I love adding chocolate chips to these high-protein muffins, and since I want my muffins to have no refined sugar, I choose sugar-free chocolate chips.

My favorite way to add them is to sprinkle them right over the tops of the muffins just before baking.

I’ve found that if I stir the chocolate chips into the batter, they tend to sink to the bottom while the muffins bake.

Sprinkling them on top gives you a delicious little bit of chocolate in every bite—and makes the muffins look pretty, too!

Lily’s milk chocolate chips is a great option, and I especially like the dark chocolate chips I find at Sam’s Club.

Use whichever sugar-free chocolate chips you love.

And there you have it!

A batch of moist, sweet, chocolate-chip zucchini muffins that are gluten free, low carb, packed with protein, and made without refined sugar.

I think you’re going to love this healthy sweet treat as much as I do.

These are easily my favorite chocolate chip zucchini muffins!

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The Secret to Moist Zucchini Muffins

A plate of moist protein zucchini muffins with chocolate chips.

Easy Variations

Once you’ve made these protein zucchini muffins, you may find yourself wanting to make them again and again!

The basic recipe is delicious on its own, but it’s also easy to change things up depending on what you’re craving or what you have in your pantry.

Here are a few fun ways to give your next batch a little something different:

  • Chocolate chips – Because chocolate makes everything better! Add sugar-free chocolate chips for a little extra sweetness and chocolatey goodness.
  • Chopped walnuts or pecans – Stir in your favorite nuts for a little crunch and added texture.
  • White chocolate chips – For a sweeter, creamy twist, try sugar-free white chocolate chips.
  • Blueberries – Fresh or frozen blueberries add little bursts of juicy sweetness to every bite.
  • Extra spices – Give these muffins a cozy fall twist with a little extra cinnamon, along with nutmeg, ginger, or allspice. Alternately you can use a pumpkin spice protein powder.

How to Store & Freeze Them

One of my favorite things about these protein zucchini muffins is how beautifully they freeze!

If you’re not planning to eat them all right away, you have a few easy options.

At room temperature, you can store the muffins in an airtight container for a day or two.

For longer storage, place them in an airtight container and keep them in the refrigerator, where they’ll stay fresh for about 4–5 days.

But if you ask me, the freezer is the way to go!

I like to freeze my muffins in an airtight container so they’re ready whenever I’m craving a sweet treat.

There’s no need to thaw the whole batch—just grab one whenever you want one.

  • To thaw on the countertop: Simply take a muffin out of the freezer and let it come to room temperature.
  • In a hurry? Place the frozen muffin on a microwave-safe plate and microwave it uncovered for about 30 seconds. It’ll be ready to enjoy in no time!
  • For an easy grab-and-go snack: Keep a few muffins frozen and take one out whenever you need a quick breakfast, afternoon snack, or healthy sweet treat. They’re perfect for busy mornings or when that chocolate craving hits!

I love knowing there’s always a delicious, protein-packed muffin waiting for me in the freezer.

It makes enjoying a homemade sweet treat so easy!

Frequently Asked Questions

Can I use frozen zucchini? Yes! Just be sure to drain off the excess liquid that forms when the zucchini thaws. Add the liquid back into the batter a little at a time as needed while stirring, being careful not to add too much—you want the batter moist, but not overly wet.

Do I need to peel the zucchini? Nope! There’s no need to peel the zucchini before shredding it. The skin is tender and blends right into the muffins, adding a little extra color and keeping the recipe nice and simple. Just wash the zucchini well, trim off the ends, and grate it with the skin on.

Do I need to squeeze the zucchini dry? No! In fact, you’ll want to keep the natural moisture from the freshly shredded zucchini because it’s one of the secrets to making these muffins so wonderfully moist. Simply add the finely shredded zucchini along with the liquid from shredding directly to the batter.

What protein powder works best? For the best texture and flavor, I recommend using a whey vanilla protein powder that you already enjoy the taste of. Since protein powders vary in sweetness and how much liquid they absorb, the brand you use can affect the final texture of the muffins. I prefer Just Ingredients Vanilla whey protein powder.

How much protein is in each muffin? Each protein zucchini muffin contains 7.7 grams of protein, making it a satisfying, protein-packed option when you’re craving something sweet.

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Woman holds half a protein zucchini muffin with chocolate chips over a charcuterie board with protein muffins.
Michelle Dickson

Protein Zucchini Muffins

These sweet, moist zucchini muffins are the perfect healthy sweet treat! They’re packed with more protein than a traditional muffin, plus they’re gluten free and low carb. With a delicious texture and just the right amount of sweetness, these muffins are the perfect treat you can feel good about enjoying.
Prep Time 15 minutes
Cook Time 22 minutes
Total Time 37 minutes
Servings: 22 servings
Course: Dessert, Snack
Cuisine: American
Calories: 129

Ingredients
  

Dry Ingredient
  • 1 cup super fine almond flour
  • 1 cup Vanilla Protein Powder Just Ingredients has no refined sugar
  • 1/2 cup coconut flour
  • 1 tsp baking soda
  • 1 tbls cinnamon, ground
  • 1/2 tsp salt
  • 3/4 cup organic monk fruit sweetener
Wet Ingredients
  • 4 large eggs
  • 1/3 cup tahini
  • 2 tbls milk or almond milk
  • 1 tsp vanilla, pure
  • 1/3 cup melted coconut oil, cooled
  • 2 1/2 cups zucchini, finely shredded
Optional
  • 3/4 cup chocolate chips, no sugar such as Lilys
  • 1/2 cup pecans, chopped

Method
 

  1. Preheat oven to to 350°. Place paper liners in muffin pan.
Dry Ingredients
  1. Place almond flour, coconut flour, vanilla protein powder, baking soda, cinnamon, salt and monk fruit in a large mixing bowl. Whisk until well combined.
Wet Ingredients
  1. Place eggs, tahini, milk, vanilla, melted coconut oil, in a medium mixing bowl and whisk together.
Combine Wet & Dry Ingredients
  1. Combine the dry and wet ingredients and stir until well combined. Batter will be stiff. Then add the finely shredded zucchini and any liquid that has formed into the batter. Stir until well combined.
Prepare to Bake
  1. Scoop into lined muffin pans, filling about 3/4 of the way. Sprinkle with chocolate chips on top of the zucchini batter, if desired.
Bake
  1. Place in a 350° oven and bake for 20-24 minutes. I find 22 minutes to be perfect for my oven.
    Remove from pan and place on a rack to cool.

Notes

One zucchini muffin is 129 calories and has 7.7 grams of protein, 2.3 grams of net carbs, and 9.7 grams of fat.
These muffins will stay fresh in the fridge for 3-4 days in an airtight container. You can also store them in the freezer in an airtight container.
I like to keep mine in the freezer and remove one at a time and microwave for 30 seconds to thaw whenever I want a sweet treat without the guilt.

You’ve Got to Try These!

Zucchini overload + a sweet craving = the perfect excuse to make these muffins!

I love that this recipe turns all that fresh summer zucchini into something sweet, delicious, and satisfying.

They’re moist, protein-packed, low carb, gluten free, and made without refined sugar, so you can enjoy a treat without feeling like you’re missing out.

Make a batch now, tuck a few in the freezer for later, and you’ll always have a homemade sweet treat ready when that craving hits.

Let me know if you love these protein zucchini muffins as much as I do!

Please share your tips and ideas with us.

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Pinterest image, woman holding half a protein zucchini muffin with creamy dark chocolate chips over a tray of healthy gluten-free high protein muffins.

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