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These Quinoa Egg Bites are the perfect mini casseroles for breakfast as you head out the door each morning. They take less than 30 minutes to bake and contain protein-packed ingredients like egg and quinoa with a little salsa on top for a spicy kick.

Mornings can be hectic, but these quinoa breakfast bites make it easy to enjoy a healthy breakfast that’s full of protein. These egg cups are great for meal prep, plus they are gluten-free and dairy-free. Pour yourself a mug of coffee and grab a few of these for a filling breakfast with minimal effort.
If you like these egg bites, you will love my avocado keto egg muffins and pizza egg muffins!
Table of Contents
Why You’ll Love This Recipe
- Protein-Packed Breakfast: These delicious bites are full of protein thanks to the eggs and quinoa in the recipe. The protein helps fill you up and keep you full for a longer period of time.
- Perfect for Meal Prep: This recipe makes a dozen egg quinoa muffins. You can store them and enjoy them for breakfast throughout the week or make a large batch and freeze them for later.
- Easy to Customize: These quinoa cups are so easy to tailor to your tastes. You can use different salsas, add more vegetables, or add toppings to change up the flavor.
Ingredients

- Quinoa: This gluten-free grain is higher in protein and lower in carbs than many other grains. It’s great for breakfast because it energizes you and keeps you full for a longer period of time. You can also use other cooked grains like brown rice, bulgar, or even this easy cauliflower rice recipe.
- Eggs: This recipe uses a combination of egg whites and egg yolks for added protein and to hold the bites together. Six egg whites have more protein than three whole eggs, so this recipe uses egg whites and just two yolks. You can use swap the egg whites and egg yolks by using 4 whole eggs if you prefer.
- Salsa: Add a little spice to these quinoa breakfast bites with a thin, not chunky salsa.
- Cumin and Garlic Powder: Season your egg bites with a little bit of cumin and garlic powder to make them more flavorful.
See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.
Variations & Dietary Modifications
- Add Vegetables: These quinoa and egg cups are a great way to sneak in some veggies for breakfast! Add leafy greens like kale, spinach, or broccoli. You can also give them a little crunch with bell peppers like in my egg white bites recipe.
- Pack in More Protein: You can also add meat to these egg bites for a little more protein. Try breakfast meats like sausage, ham, or bacon, or your favorite lunch meat.
- Make Them Cheesy: If you don’t need these quinoa muffins to be dairy-free you can also add cheese! Swiss cheese, feta, cheddar, and goat cheese are all great options.
How to Make Quinoa Egg Bites
Before preparing your quinoa egg cups, you need to cook the quinoa according to the instructions on the package. Once the quinoa is cooked, preheat your oven to 325°F while you prepare the egg bites.

Step 1: Mix the Ingredients. Combine the egg whites, egg yolks, seasonings, and cooked quinoa in a large mixing bowl.

Step 2: Fill the Muffin Tin. Pour the mixture into the 12 muffin cavities of a well-greased muffin tin. Fill each muffin well ¾ of the way full.

Step 3: Add the Salsa. Add 1-2 tablespoons of salsa to each muffin well and stir it in to disperse it.

Step 4: Bake the Bites. Bake the quinoa egg muffins for 20-25 minutes at 325°F until the edges turn slightly brown. Remove them from the oven and allow them to cool.
Expert Tips
- Rinse Your Quinoa: Rinsing quinoa before cooking it helps remove some of the bitter flavor, so it’s always best to give the quinoa a good rinse before preparing it.
- Don’t Use Chunky Salsa: This recipe works best with a thin salsa versus a chunky salsa. The chunky salsa will sink to the bottom of the cups instead of staying on top.
- Keep Them From Sticking: Make sure your quinoa cups lift out of the muffin tins easily by using paper or silicone cupcake liners in addition to spraying the cups with nonstick cooking spray.
Storage Directions
- Storing: Keep these quinoa with eggs in an airtight container in the refrigerator for up to 5 days. These bites also freeze well and can stay in the freezer for a month. Wrap each bite individually with plastic cling wrap to help keep the moisture out when you freeze them.
- Reheating: Heat up your quinoa and eggs in the microwave for 30 seconds. You can also reheat them in the oven at 325°F for 3-5 minutes. Be sure to thaw frozen quinoa bites in the refrigerator overnight before reheating.
- Make Ahead: Preparing the quinoa is the most time consuming part of this recipe, so you can make the quinoa the day before to save time. Store the quinoa in an airtight container in the refrigerator overnight and then make these cups the next day.

Serving Suggestions
Enjoy quinoa for breakfast with eggs with these delicious quinoa egg bites! They are the perfect grab and go breakfast for a busy morning. Quinoa and eggs are packed with protein and will help keep you full and energized as you conquer your morning to-do list. They also make a healthy post-gym snack when you need a little boost to get you through the rest of the day!
- Enjoy these delicious egg quinoa muffins for breakfast with a cantaloupe citrus smoothie or a high protein smoothie as you head out the door.
- Try these bites as part of a sit-down breakfast with some banana chocolate chip pancakes and a classic Waldorf salad.
- Pair these quinoa bites with your favorite latte in the morning. They taste better than the ones at a coffee shop.
Quinoa Egg Bites Recipe FAQs
The quinoa does need to be cooked before adding it to these breakfast bites. You can prepare it in advance or right before adding it to the eggs. Just let it cool for a bit so it doesn’t prematurely cook the eggs.
This meal prep breakfast recipe is perfect for doubling or tripling to make a month’s worth of breakfasts. You will need a few muffin tins and a bigger bowl to make more!
Yes, quinoa is a gluten-free grain. Be sure to read the packaging to ensure your quinoa wasn’t processed with gluten and is truly gluten-free.

More Delicious Breakfast Quinoa Recipes
If you tried this Quinoa Egg Bites recipe or any other recipe on my website, please leave a 🌟 star rating and let me know how you go in the 📝 comments below.

Quinoa Egg Bites with Salsa
Ingredients
- 1 1/2 cups Quinoa, cooked
- 6 Egg whites
- 2 Egg Yolks
- 1 teaspoon Cumin
- 1 tablespoon Garlic Powder
- 3/4 cup Salsa
- Salt and Pepper, to taste
Instructions
- Cook the quinoa according to package instructions then set aside to cool. Preheat oven to 325 F. Generously spray a muffin pan with cooking spray.
- In a large mixing bowl, combine all the ingredients except the salsa. Stir together to mix well.
- Divide the mixture among 12 muffin cavities, filling each cavity 3/4 of the way full.
- To each cavity, add 1-2 tbsp salsa stirring the salsa into the egg/quinoa mixture to disperse.
- Bake the quinoa egg muffins 20-25 minutes until edges are slightly browned. Remove from the oven and cool slightly before enjoying!
Video
Notes
- Rinse the quinoa before cooking it to remove some of the bitter flavor.
- Use a thin salsa so it stays near the top of the bites instead of sinking to the bottom.
- Spray well or use cupcake liners to make sure your quinoa cups lift out of the muffin tins easily.
- Reheat leftovers in the microwave for 30 seconds. Store leftovers in the refrigerator up to 5 days or store in the freezer up to 30 days.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
I love the addition of quinoa in these! Extra nutrition and extra yum!
Lots of extra goodness. Thanks for linking my oatmeal too!
Man I love eggs (and breakfast). I usually have eggs and mushrooms every day and have been for like 2 years. I CAN’T STOP.
Same here! I can’t remember the last time I didn’t have eggs for breakfast.
I love eggs for breakfast and I almost always pair them with something spicy, so I love the idea of these muffins!
You just gave me an idea Lisa. Sriracha!
I’ve actually ALWAYS been a breakfast person. I wake up and want something almost immediately!
These muffins sound GREAT though. My husband is a lazy breakfast eater, so he would love these. I don’t mind taking the extra time to make something in the am, but on the mornings I am running late (like today…) these would have been perfect. Pinning! Happy Monday Megan!
They’re nice to have on hand for busy mornings. Happy new year Ashley!
Great recipe Megan! Can’t wait to try it. 🙂
Thanks Daisy, happy new year!
I love eggs for breakfast and Egglands best are the only ones I eat too. Putting quinoa inside of the muffins is a great idea!
They’re great right after a hard workout.
Oooooh I love this as I LOVE ME SOME ALL THINGS EB EGGS 🙂
Thanks Carla, EG eggs are the best!
I used to make egg muffins for Alex all the time. These sound so good (you know you had me at salsa and egg whites :D)
You must like spicy things like me!
I can’t wait to try these! Some mornings I just don’t have it in me to ACTUALLY make a decent breakfast, and this would be such an awesome thing to have on hand, for me or for my toddler!
They’re definitely a big time savior. Hope you like them Morgan!
I absolutely love egg muffins and now I want to make some! So perfect for on the go – too bad my poached or fried eggs don’t travel so well, lol 🙂
Right? That’s why I had to come up with something filling for on-the-go and they’re good cold too.