September 24, 2021


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Easy Low Carb Mini Pizza Muffins Recipe with Zucchini

7 min read

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If you are a zucchini lover, you should be very excited right now because I’m about to shower you with low carb zucchini recipes! Let’s start with this low carb pizza muffins recipe.

We are celebrating one of my favorite times of year today: Zucchini Season!

I love zucchini so much that I’ve been planning for it for weeks. True story.

This time also happens to coincide with the season for a lot of other fresh produce, making me love it that much more. Maybe they should change what “it’s the most wonderful time of the year” refers to…

You’ll get to enjoy my favorite pizza muffins recipe, a delicious au gratin casserole, and more… all made low carb thanks to zucchini!

The only problem with this week is deciding which low carb zucchini recipes to feature on the blog. These baked keto zucchini fries are super popular! There are just so many yummy options, but I’ve narrowed it down to my favorite five for you.

You’ll be able to find a mix of sweet and savory recipes, starting with this easy low carb pizza muffins with zucchini recipe. But make sure you also try these other low carb zucchini recipes:

Zucchini pizza bites are most commonly served as a starter (and indeed, they make a great low carb appetizer idea), but they don’t have to be.

I’ve enjoyed these easy pizza muffins for lunch many time before! They are delicious, filling, and easy to have ready in advance. That makes them ideal for on-the-go snacks or a quick meal.

That was the primary reason to turn them into mini low carb pizza muffins in the first place.

This low carb baked zucchini pizza bites recipe is so easy to make. They are perfectly portable healthy snacks, appetizers, even breakfast or lunch.

How To Make Pizza Muffins With Zucchini

One of the more common ways to make baked zucchini pizza bites in the oven is to simply slice zucchini, add oil and seasoning, roast, add pizza toppings, and roast a little longer.

Basically, that method shares similarities with how to make eggplant pizzas.

However, this pizza muffins recipe is a little bit different. This recipe is easily made ahead and taken along with you.

Making mini meals in muffin pans has always worked out well in my experience. These alternative zucchini pepperoni pizza muffins were a great way to use my mini muffin pan! I lined it with parchment paper cups for no-mess cleanup.

So what does this pizza muffins recipe call for?

As you can see, there is just a small amount of coconut flour needed to make these mini pizza muffins. I really don’t recommend replacing that with another flour, because its main purpose is to absorb moisture and no flour does that as well as coconut flour.

The coconut flour is a great addition, because it means you won’t have to squeeze the moisture out of the zucchini (which is really kind of a pain, so yaaaay for an easy keto pizza bites recipe).

Pepperoni pizza is by far my favorite (I usually make it on fathead pizza crust or sometimes cauliflower pizza crust) which is why this recipe is for pepperoni pizza muffins. I use mini pepperonis here, but if you can only find bigger ones, just cut them into smaller pieces.

Don’t be afraid to unleash your creative side! Ultimately, this is your pizza muffins recipe and you can make sausage pizza, veggie pizza, 4-cheese pizza, or anything else you’d like. The sky is the limit here, friends!

Here are a few tips to get the yummiest low carb pizza muffins possible:

Use the right amount of zucchini

This recipe calls for 2 medium zucchini, which is about 2 cups once it’s shredded. That’s 2 cups loose in the measuring cup, not pushed down… so use a gentle hand or they’ll be way too watery.

Beware of watery zucchini

Yes, each squash will be unique. If your zucchini is very watery after shredding, squeeze it gently to get rid of the extra water. No need to do it very hard or get every last drop out, just make sure it’s not dripping wet (because you’re using coconut flour to help with this, remember?)

Adjust coconut flour as needed

The coconut flour is there to make this an easy low carb pizza muffins recipe where you don’t have to worry too much about all the extra liquid. That means if your batter is watery even after the tip above, you can add a little more coconut flour to thicken it up.

Your mixture should be fairly thick. A little coconut flour goes a long way, so if you need to add more, add only a teaspoon at a time, stir, and wait a couple minutes for it to thicken. Really… don’t rush this part!

You don’t want soggy pizza muffins, but you don’t want super dry ones, either.

Flatten your muffin tops

When you’re making traditional keto muffins, everyone loves the rounded muffin top.

However, with low carb pizza muffins, you want to flatten the top. This ensures that the sauce and toppings stay on afterward.

No one wants to have their pepperoni sliding off their keto pizza bites. That would be utterly tragic.

Don’t over fill the muffin cups

If you fill the muffin cups too much, you’ll have too much muffin for the amount of toppings you can fit on them.

Just distribute your zucchini batter evenly among 20 cups and you’ll be just right (hint: that’s about half way full).

How To Store This Low Carb Pizza Muffins Recipe

This pizza muffins recipe is a good one to make ahead. They’ll keep in the fridge up to a week and even be good straight out of the freezer.

If you freeze them, make sure to bake them first. Then, when you take them out to thaw, you can add your toppings and bake to eat. It’ll be like having your own mini low carb personal pan pizza crusts ready and waiting for you.

So how will you customize this pizza muffins recipe? Are you a meat lovers kind of a person or are you all about the veggies? Perhaps you’ll make a variety and eat one of each!

Leave a comment and let me know your favorite kind of keto pizza toppings.

This low carb baked zucchini pizza bites recipe is so easy to make. They are perfectly portable healthy snacks, appetizers, even breakfast or lunch.

Reader Fave Keto Recipes

The recipe card is below! Readers also made these similar recipes after making this one.


This low carb baked zucchini pizza bites recipe is so easy to make. They are perfectly portable healthy snacks, appetizers, even breakfast or lunch.

Easy Low Carb Mini Pizza Muffins Recipe with Zucchini

This low carb pizza muffins recipe with zucchini is so easy to make. They make perfectly portable zucchini pizza bites for healthy snacks, appetizers, even breakfast or lunch.

Prep Time 15 minutes

Cook Time 20 minutes

Total Time 35 minutes


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RECIPE TIPS + VIDEO in the post above, nutrition info + recipe notes below!

Click on the times in the instructions below to start a kitchen timer while you cook.

  1. Preheat the oven to 375 degrees F (191 degrees C). Line 20 cups of a mini muffin pan with parchment or silicone liners.

  2. In a large bowl, stir together the shredded zucchini, shredded mozzarella, coconut flour, sea salt, and black pepper. Stir in the eggs and melted butter.

  3. Transfer the zucchini mixture evenly into the lined muffin cups, packing down and making sure the top is flat.

  4. Bake for 18-22 minutes, until the top is golden and firm. If the bites puffed up like muffins, let them cool for a few minutes to flatten out again.

  5. Spoon a teaspoon of marinara sauce onto each zucchini bite, then top with remaining mozzarella cheese. Sprinkle with Italian seasoning. Add pepperoni slices.

  6. Place under the broiler for 2-3 minutes, until the cheese is melted and golden.

Recipe Notes

Nutrition info will vary slightly depending on what marinara sauce you use.

Serving size: 2 mini pizza muffins

Nutrition Information Per Serving

Nutrition Facts

Amount per serving. Serving size in recipe notes above.

Calories 117

Fat 8g

Protein 8g

Total Carbs 4g

Net Carbs 3g

Fiber 1g

Sugar 1g

Where does nutrition info come from? Nutrition facts are provided as a courtesy, sourced from the USDA Food Database. You can find individual ingredient carb counts we use in the Low Carb & Keto Food List. Net carb count excludes fiber, erythritol, and allulose, because these do not affect blood sugar in most people. We try to be accurate, but feel free to make your own calculations.

© Copyright Maya Krampf for Wholesome Yum. We’d LOVE for you to share a link to this recipe, but please DO NOT COPY/PASTE the recipe instructions to social media or websites. You may share a photo with a link back instead.

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