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These baked zucchini egg muffin cups are a delicious and healthy breakfast, snack, or meal option. They are low carb protein-packed, grab and go bites that are easy to make-ahead and reheat.

Healthy Zucchini Egg Muffin Cups cooling on a wire rack.

If you love zucchini then you are in for a treat with these zucchini egg muffins!  Not only are they delicious, but they are also easy to make, and full of veggies. They are made with less than 10 ingredients ( 8 to be exact), most of which you probably already have in your kitchen.

I usually use zucchini to make recipes like zucchini lasagna or zucchini casserole. And I usually use eggs to make quiches like my famous carrot broccoli pine nut and goat cheese quiche ( oh, it is epic! ) or my gluten-free quiche Lorraine. But these egg muffin cups combine both eggs and zucchini together with the most scrumptious results.

Zucchini egg cups on wire rack.

Why this recipe works

  • Eggs are a great source of protein. Because of the ingredients, these egg muffins are naturally gluten-free and low carb/ Keto.
  • They are easily customizable to your tastes and dietary needs.
  • They are so yummy! They have an almost refined taste thanks to the way the zucchini, cheese and nutmeg melt together.
  • They are the perfect grab and go snack or breakfast.

Recipe ingredients:

Ingredients needed to make Zucchini Egg Muffin Cups.
  • Zucchini– fresh small to medium zucchini works here. Just make sure you have enough to shred into 2.5 cups.
  • Garlic powder and onion powder– any brand or kind works here. They easily adds flavor to the recipe.
  • Eggs– this recipe is made using large eggs.
  • Gruyere or Swiss cheese– either works as long as its shredded.
  • Ground nutmeg– you can grind it yourself or buy it ground.

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

Additions/ Substitutions

  • Instead of onion powder and garlic powder, you can use fresh garlic and onion. Just add it to the pan along with the zucchini while it cooks.
  • Instead of gruyere or Swiss cheese, you can use shredded Parmesan or cheddar.
  • To make this recipe Paleo, Whole30, or Dairy-free, just omit the cheese.

Step by step instructions

Shredded zucchini in a pan with spices.
Step 1

Step 1: Shred and cook the zucchini.

This is a critical step. You have to cook the zucchini because it removes the liquid from them. This stops you from having soggy egg muffins.

Also, cooking it brings out the flavor of the zucchini.

Eggs mixed together in a bowl.
Step 2

Step 2: Cook until the moisture has evaporated and the zucchini has reduced in size and it has begun to be golden in color a little bit.

Step 3

Step 3: Mix the eggs in a large bowl.

Cheese and spices added to the eggs.
Step 4

Step 4: Mix the cheese, salt, pepper, and nutmeg to the eggs.

Zucchini added to the eggs in a bowl.
Step 5

Step 5: Mix in the cooked zucchini.

Egg mixture in silicone muffin tin.
Step 6

Step 6: Pour the mixed egg mixture evenly into a silicone muffin tin.

Using a silicone muffin mold helps to avoid the egg muffins from sticking to the pan.

Freshly baked zucchini egg cups.
Step 7

Step 7: Bake

A bite taken out of zucchini egg muffins.
Step 8

Step 8: Enjoy!

Expert tips:

  • Use a silicone muffin mold OR heavily grease your muffin tin.
    • This is the only way to avoid the egg muffins from sticking to the pan.
    • Full disclosure, I’ve tried heavily greasing my regular muffin pan several times and my egg cups stuck to the pan EVERY time. I have only been able to make them using silicone molds to avoid this issue.
  • Make sure to sauté the zucchini until the moisture has been cooked out.
    • This is the best way to avoid these egg muffins from being soggy.
    • Zucchini is 90% water. That is why many zucchini recipes require draining it or squeezing out the extra moisture. Here, I find it is better to cook the zucchini to remove the moisture. You’ll literally see water evaporating from the zucchini as you cook it.

Recipe FAQs

Can you freeze these egg muffins?

Yes, these baked egg cups are freezer friendly! If you are going to freeze them, then let them cool completely.

Then wrap them up individually with plastic wrap. You can keep them in the freezer for 3-4 months.
Then just take them out of the freezer and let them thaw in the fridge overnight OR microwave them straight out of the freezer

How do you serve them?

For breakfast. These are my all time favorite breakfast egg muffins. You can eat them with fruit and bacon or sausage for a complete meal.
For lunch. Pair these egg muffins with a side salad or some roasted potatoes for a healthy lunch.
As a snack. You can just grab a few of these egg cups and eat them alone to help curb any mid-day hunger.

How do you store them?

In an airtight container in the fridge for 3-5 days.

Zucchini egg muffins stacked on top of each other.

Other breakfast recipes you’ll love:

Did you try this recipe? Please leave me a ⭐ review below!

5 from 18 votes

Healthy Zucchini Egg Muffin Cups

Servings: 12 muffins
Prep: 15 minutes
Cook: 25 minutes
Total: 40 minutes
Healthy Zucchini Egg Muffin Cups cooling on a wire rack
These baked zucchini egg muffin cups are a delicious and healthy breakfast, snack, or meal option. They are flavorful protein-packed, grab and go bites that are easy to make-ahead and reheat.

Ingredients 

  • 2 1/2 cups shredded zucchini, (2 medium zucchini)
  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 9 eggs
  • 1/2 cup gruyere or Swiss cheese
  • 1/2 teaspoon salt
  • 1/4 teaspoon pepper
  • 1/4 teaspoon ground nutmeg

Instructions 

  • Preheat oven to 350 degrees F. Grease a silicone muffin tin or a regular muffin tin with olive oil or butter. Silicone muffin tins work best to avoid the eggs sticking to the pan.
  • Add shredded zucchini to a frying pan and top with garlic powder and onion powder. Mix and spread out the shredded zucchini until almost flat on the frying pan. Cook over medium heat for 10-12 minutes, mixing every few minutes and then reflattening it. You’ll see liquid evaporating from the zucchini, this is normal. Cook the zucchini until it has browned a little and shrunken in size. Let the shredded zucchini cool for a few minutes.
  • In a large bowl, add all the eggs and mix. Then add cheese, salt, pepper, nutmeg, and the cooked zucchini. Mix again.
  • Add about 4 Tablespoons of the egg mixture to each muffin tin.
  • Bake for 23-28 minutes, until the egg muffins are set. Let the muffins cool for a few minutes and then run a knife around the edges to remove them. Eat or let them cool on a wire rack.

Notes

Note: if you are going to freeze these egg muffins, then let them cool completely after baking. Then wrap them up individually with plastic wrap. You can keep them in the freezer for 3-4 months. Then just take them out of the freezer and let them thaw in the fridge overnight OR microwave them straight out of the freezer.
  • Instead of onion powder and garlic powder, you can use fresh garlic and onion. Just add it to the pan along with the zucchini while it cooks.
  • Instead of gruyere or Swiss cheese, you can use shredded Parmesan or cheddar.
  • To make this recipe Paleo, Whole30, or Dairy-free, just omit the cheese.

Nutrition

Serving: 1egg muffinCalories: 70kcalCarbohydrates: 1gProtein: 6gFat: 5gSaturated Fat: 2gPolyunsaturated Fat: 1gMonounsaturated Fat: 2gTrans Fat: 0.01gCholesterol: 127mgSodium: 154mgPotassium: 119mgFiber: 0.3gSugar: 1gVitamin A: 267IUVitamin C: 5mgCalcium: 63mgIron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Breakfast
Cuisine: American
Tried this recipe?Mention @perchancetocook or tag #perchancetocook!
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