For a healthy keto breakfast try these zucchini protein muffins. They are low carb, high protein, sugar free and gluten free. Using protein powder adds flavor without gluten or carbs and it’s a good way to use garden zucchini! Each healthy zucchini muffin has only 4.8 grams net carbs and 12.1 grams of protein!
You might also like these chocolate protein keto balls!

As I get older I am always trying to find ways to up my protein intake and yesterday I remember this low carb zucchini protein muffins recipe. This was the perfect recipe to redo because we still have tons of zucchini from our garden and I was craving a muffin..
Not only are these zucchini muffins low carb but they are high protein and gluten free too. They are also nut free so no almond flour either nor coconut flour. I change the recipe a bit from the original to make them even easier.
All you have to do is mix and bake for easy nutritious breakfast or keto sweet snack. I use low carb chocolate chips for added flavor but later in the post I’ll show you various ways to change up the flavors.
What is the texture of these healthy zucchini muffins?
Using protein powder instead of wheat flour in baked goods sometimes makes them dry and spongy. These zucchini muffins are moist and chewy just like regular flour muffins. The key is to not bake them too long.
Below you can see what the texture looks like.

Recipe ingredients and substitutions.
I do use quite a few ingredients in these low carb protein muffins. It’s based off a soul bread recipe I used for my keto banana bread. Note these two recipes use protein powder instead of white flour, almond flour, oats, oat flour or coconut flour. It adds flavor, protein and keeps the recipe low carb and gluten free.
So all of the recipe ingredients are fresh zucchini, cream cheese, butter, eggs, olive oil, Sweetleaf vanilla drops, Swerve brown sugar sweetener, protein powder, baking powder, baking soda, salt, cream of tartar, flaxseed meal and ChocZero keto chocolate chips.
- protein powder – Originally I used Isopure Zerocarb Vanilla protein powder for this recipe because I like the taste and it has zero carbs. This time I used Clean Simple Eats Cake Batter protein powder. I really love the flavor of this protduct, especially for keto baked goods. It does have 7 carbs per scoop compared to the 0 carbs of Isopure but I wanted to try it and it was tasty. However you can use whatever protein powder you want. Just be mindful it may affect the texture of the finished recipe.
- Choczero chocolate chips – Orginally I used Lily’s chocolate chips but I’m finding it hard to get those lately and I really like Choczero’s chips. You can substitute with dark chocolate bar shavings or dark chocolate chips. You will just have to account for the carbs if you are on a low carb diet. I have more ideas below.
- brown sugar sweetener and stevia drops – I used Swerve brown sugar sweetener which is my favorite sweetener. You can use any brand of sweetener you want but if you can use a brown sugar flavored one that is best. Lakanto Golden is one of them. And if you don’t care about carbs just use regular brown sugar. Also I love SweetLeaf vanilla stevia drops because they add a lot of sweetness and a vanilla extract flavor. But if you don’t have it you can add ½ cup more sweetener.
- cream of tartar and ground flaxseed – Cream of tartar is a little unusual but you can find this at bigger grocery store in the spice or baking aisles. Ground flaxseed is found in many stores and I buy mine at Aldi. You want ground flaxseed not the whole seed form.
- cream cheese, butter, eggs and olive oil – These are very common ingredients and you probably have them already. I would not substitute as they add a good dose of fat to balance the texture of the protein powder and adds to the taste.
In my original recipe I used xanthan gum too which is great for keto baked goods but I didn’t have any today and they were still good so I think you can skip it you want. I had used ½ teaspoon in this recipe if you want to use it and have it on hand.
So while you might need to initially purchase a few things, you will definitely use them. You can find these gluten free, low carb baking ingredients in my Amazon storefront.
How to make zucchini protein muffins.
Step 1: First thing you need to do is shredded the zucchini with a hand grater. Place the zucchini into a tea towel or a bunch of paper towels and squeeze as much water out of the zucchini as you can.
Step 2: Next add the cream cheese and butter to a microwave safe bowl and microwave for 30 seconds. Place them into a large mixing bowl and blend together with a hand mixer.
Step 3: Next add in the wet ingredients: eggs, liquid stevia, olive oil as well as the Swerve brown sugar sweetener and blend well. Lastly fold in the grate zucchini.
Step 4: In a separate bowl mix the dry ingredients: 2 scoops protein powder, baking soda, baking powder, cream of tartar, salt, and ground flaxseed meal. Pour the dry ingredients into the wet ingredients and stir by hand. Fold in the chocolate chips.

Step 5: Spray a muffin tin with non-stick cooking spray and then spoon the muffin mixture into the muffin cups. Bake in a preheated 350°F oven for 15-20 minutes until golden brown and a toothpick comes out clean.

Baking time will vary depending on the size of your muffin tin so check them towards the end. Mine took 16 minutes.
Step 6: Place the muffin pan on a wire rack and let them cool completely before eating. Store them an air-tight container and they should last for quite a few days.

These freeze well too. Just reheat in the microwave for a 10-30 seconds. Scroll down to for recipe tips for changing the flavor of these muffins. Please also scroll down to view the printable recipe card.
Recipe Notes and Substitutions
- It is very important that you squeeze out as much of the water from the zucchini as you can. I just place the shredded zucchini into a tea towel and squeeze it out over the sink. When you are done the zucchini show be stuck together in a big clump.
- I used Lily’s chocolate salted caramel chips for added flavor but you can try Chocozero dark chocolate chips for another keto alternative. Both are low in net carbs and are another way to add flavor.
- You could also add other flavors through your protein powder. I used a vanilla flavor but you can try chocolate, banana or whatever flavor you want. Note that I use Isopure Zerocarbs because it doesn’t have carbs and it’s the only whey protein powder I have use this recipe with.
- Another idea is to use different flavor extracts. A vanilla extract or maybe caramel, lemon, maple, raspberry etc would be great. I’ve added them to my Amazon storefront to check out.
- When mixing the bread it is important that you only use a mixer on the wet ingredients and just to hand mix the dry ingredients to keep the light texture.
- Lastly you can add nuts, seeds, unsweetened coconut, cacao nibs, and any other low carb mix ins for added flavor. You can also play around with low carb berries like blueberries, blackberries and strawberries. Spices like cinnamon, pumpkin pie spice, etc would also be nice.

Other high protein low carb recipes.
If you enjoy the added boost of protein in your keto recipes here are 29 protein powder recipes. Below are a few of my favorites.
- keto peanut butter banana pudding
- coconut cake protein balls
- creamy chocolate gelatin squares
- peanut butter banana fudge
- berry chia seed pudding
- chocolate pudding protein popsicles
- banana bread granola
Well I hope you give these low carb zucchini protein muffins a try. They are really tasty and versatile. There is nothing like a warm muffin a bit of butter for a keto sweet snack or healthy breakfast. And they freeze well too so they are great for meal prep.
The nutritional information and carb count for 1 muffin is 148 calories
8.9g fat / 6.2g carbs / 1.4g fiber / 12.1g protein = 4.8g net carbs

Zucchini Protein Muffin Recipe (low carb, gluten free)
Looking for a keto sweet snack or breakfast? Try these zucchini protein powder muffins which are gluten free, low carb, high protein and sugar free. This healthy muffin recipe makes for moist, sweet and delicious zucchini muffins.
Ingredients
- 3 ounces cream cheese
- 2 tablespoons butter
- 2 eggs
- 1 cup zucchini, shredded (water squeeze out)
- 2 tablespoons olive oil
- ½ teaspoon liquid stevia (if you don't have, substitute with ½ cup more of sweetener)
- ½ cup Swerve brown sugar sweetener
- 2 cups protein powder (I used Clean Simple Eats Cake Batter protein powder)
- ¼ teaspoon baking soda
- 1 ¼ teaspoon baking powder
- ¼ teaspoon cream of tartar
- ¼ teaspoon salt
- 2 tablespoon ground flax meal
- ¼ cup keto chocolate chips (I used ChocZero brand)
Instructions
- Preheat oven to 350°F. First thing you need to do is shredded the zucchini with a hand grater. Place the zucchini into a tea towel or a bunch of paper towels and squeeze as much water out of the zucchini as you can.
- Next add the cream cheese and butter to a microwave safe bowl and microwave for 30 seconds. Place them into a large mixing bowl and cream together.
- Add in the wet ingredients: eggs, liquid stevia, olive oil as well as the Swerve brown sugar sweetener and zucchini.
- In a separate mixing bowl, mix the dry ingredients: protein powder, baking soda, baking powder, cream of tartar, salt and ground flaxseed meal. Then pour them inot the wet ingredients and stir by hand. The batter will be a bit runny but it’s ok.
- Spray a muffin pan with nonstick cooking spray and then spoon the batter into muffin tin.
Add the chocolate chips separately. Because the batter is thin, they tend to sink to the bottom when baking but it is still tastes delicious. - Bake for 15-20 minutes. Cooking times will vary depending on the size of your muffin tin so check them towards the end. Mine took 16 minutes.
- Let them cool completely before eating. Store them an airtight container and they should last for quite a few days.
Notes
Recipe Tips & Notes
- It is important that you squeeze out as much of the water from the zucchini as you can. I just place the shredded zucchini into a tea towel and squeeze it out over the sink. When you are done the zucchini show be stuck together in a big clump.
- When mixing the bread it is important that you only use a mixer on the wet ingredients and just to hand mix the dry ingredients to keep the light texture.
- I used Chocozero milk chocolate chips which are low in net carbs.
- You could also add other flavors through your protein powder. I used cake batter but you can try chocolate, banana or whatever flavor you want. Note that I use originally used Isopure Zerocarbs because it doesn’t have carbs but this time I used Clean Simple Eats Cake Batter and it has a few more carbs but I love the flavor.
- Another idea is to use different flavor extracts. A caramel extract or maybe lemon, maple, raspberry etc would be great. I’ve added them to my Amazon storefront to check out.
- Lastly you can add nuts, seeds, unsweetened coconut, cacao nibs, and any other low carb mix ins for added flavor.
The nutritional information and carb count for 1 muffin is 148 calories
8.9g fat / 6.2g carbs / 1.4g fiber / 12.1g protein = 4.8g net carbs
Nutrition Information:
Yield: 12 Serving Size: 1Amount Per Serving: Calories: 148









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