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.

Healthy Zucchini Egg Muffin Cups cooling on a wire rack

You have got to try these zucchini egg cups! Not only are they incredibly delicious, but they are also easy to make and full of veggies. They are made with less than 10 ingredients ( 8 to be exact, including salt and pepper), most of which you probably already have in your kitchen.

They are also naturally gluten-free and low carb, and easily customizable to your tastes and dietary needs.

zucchini egg cups on wire rack

If you love zucchini then you are in for a treat!

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 I have not paired together zucchini and eggs and I am so glad that I did in this recipe because it is amazing.

So, if you are looking for recipes with zucchini and eggs, then look no further!

These savory zucchini egg muffins have an almost refined taste thanks to the way the zucchini, cheese and nutmeg melt together.

Ingredients needed:

  • zucchini
  • garlic powder
  • onion powder
  • eggs
  • gruyere or Swiss cheese
  • salt
  • pepper
  • ground nutmeg
zucchini egg muffins stacked on top of each other

Dietary and ingredient swaps:

To make Paleo, Whole30, or Dairy-free. Omit the cheese.

To make with fresh garlic and onion. If you use fresh garlic and onion instead of garlic powder and onion powder, just make sure to cook it along with the zucchini.

To make with a different cheese. Parmesan and cheddar would work great here. I personally like how the nutmeg and gruyere/Swiss flavors work together.

How to make these zucchini egg muffin cups:

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.

Step 2) Mix all of the ingredients into the eggs

You basically put ALL of the ingredients here into a large bowl and mix.

Step 3) Pour into muffin tin

I suggest using a silicone muffin mold to avoid the egg muffins from sticking to the pan.

Step 4) Bake

Step 5) Eat or Freeze

Eat them right away or freeze them for later.

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.

breakfast egg muffins cooling on wire rack

Recipe tips:

How to avoid the egg muffins from sticking to the pan.

Use a silicone muffin mold OR heavily grease your muffin tin.

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.

How to avoid soggy egg muffins because of the zucchini.

Sautée it!

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.

Make sure it has begun to golden in color and overall has reduced in size prior to adding it to your eggs.

bite taken out of zucchini egg muffin cups

How to 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.

Other breakfast recipes you may enjoy:

Cherry Mango Carrot Smoothie with Greek Yogurt

Paleo Gluten Free Spinach Bacon Quiche

Banana Oatmeal Chocolate Chip Cookies

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.

Healthy Zucchini Egg Muffin Cups cooling on a wire rack
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Healthy Zucchini Egg Muffin Cups

Servings: 12 muffins
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes

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.
Calories: 72kcal, Carbohydrates: 1.6g, Protein: 5.9g, Fat: 4.8g, Cholesterol: 128mg, Sodium: 162mg
Course: Breakfast
Cuisine: American
Keyword: zucchini egg muffin cups