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Quinoa Salsa Egg Muffins are a simple protein packed breakfast loaded with flavor and spice for an easy breakfast you can meal prep and take with you on the go! Gluten Free + Low Calorie

Breakfast hasn’t always been the easiest meal of the day for me. For years, I did not eat anything for breakfast. By the time lunch rolled around or late night, I was eating everything and anything in sight. Because I was hungry and not fueling my body properly!
It wasn’t until I changed my eating habits and lost 80 pounds many years ago that I realized how eating breakfast was key to managing my hunger. Getting nutrients, particularly protein, in my body first thing in the morning prevented me from overeating later in the day.
These Healthy Quinoa Salsa Egg Muffins are delicious and perfect for meal prep. They’re balanced with protein, fat and carbs and you can take them with you on the go!

Why These Low Calorie Egg Muffins Are Better For You
To make this a nutritionally balanced meal, I added quinoa as a carbohydrate source. Many egg muffins have vegetables making them a lower carb meal. However, adding a starchy carbohydrate like quinoa actually makes them better balanced and more satisfying!
- Low Calorie – Each quinoa egg muffin is only 100 calories. I recommend eating about 3 making this only a 300 calorie meal. But it’s a 300 calorie meal that’s better balanced with all 3 food groups!
- Higher Protein – Each egg muffin has 7 grams of protein! That is amazing and the quinoa and egg whites are to thank for that!
- Gluten Free – The ingredients are naturally gluten free in this recipe.
- Lower Carb – Because quinoa is higher in protein, the recipe is lower in carb with only 14 grams per egg muffin. While the egg muffins are more satisfying and filling with the quinoa, they are still carb conscious for those who need to be.

Quinoa Salsa Egg Muffin Ingredients
Here’s what you need to make these delicious and healthy egg muffins! You’ll also need a muffin tin. I used this muffin pan and sprayed the pan with cooking spray, but I like to use a silicone muffin pan too as they tend not to stick as much in those.
- Quinoa, cooked
- Egg Whites
- Egg Yolks
- Salsa
- Garlic Powder
- Cumin
- Salt + Pepper

How To Bake Egg Muffins with Quinoa
The detailed instructions on how to make egg muffins with quinoa are below in the recipe card, but here are the brief instructions. They’re actually very easy and perfect for freezing for future meals!
Step One – Cook the quinoa according to package instructions then set it aside to cool. Preheat oven to 325 F and prepare a muffin pan.
Step Two – Stir together all the ingredients except the salsa in a large mixing bowl.
Step Three – Divide the mixture among 12 muffin cavities, filling each cavity 3/4 of the way full.
Step Four – Add the salsa to each muffin cavity. You can add it in step two, but I found it disperses more evenly when you take the time to do it individually.
Step Five – Bake the muffins, cool briefly and enjoy!

How To Store Egg Muffins
Store leftover Quinoa Egg Muffins in the refrigerator in a sealed container. They may be kept up to 5 days. You can also keep them in the freezer up to 30 days.
I recommend wrapping each egg muffin with plastic wrap then storing in a plastic bag. This will prevent some of the moisture from getting into the egg muffins. It certainly won’t prevent all of it, but it does help!
How To Reheat Gluten Free Quinoa Egg Muffins
Reheat quinoa egg muffins from the refrigerator in the microwave for 30 seconds. You can also bake them in the oven at 325 F for 3-5 minutes or until warm.
If you froze your egg muffins, be sure to thaw them first by taking them out of the freezer and placing in the refrigerator overnight. Then reheat them in the microwave or oven.
Quinoa Egg Muffins Recipe Substitutions
Here are substitutions you can make to customize your quinoa egg muffins. Remember when you make substitutions, it does change the nutritional values from what you see in the recipe card at the end of this blog post.
- Egg Whites – You can swap egg whites with whole eggs by dividing the egg whites in half. If you do this, it will reduce the protein significantly (i.e. 6 egg whites has more protein than 3 whole eggs) and increase the calories as fat has more calories per gram than protein.
- Egg Yolks – You can substitute the yolks with egg whites by doubling the yolks.
- Quinoa – Any cooked grain may be used in place of quinoa. Bulgur, amaranth, brown rice, barley, freekeh would work well.
- Spices – The spices may be omitted or replaced with other fresh or dried herbs and spices like cilantro or parsley. I find egg muffins are bland without spices.
- Salsa – Any thin salsa green or red works in this recipe. I do not recommend using a chunky salsa as it will place too much weight on the batter and the egg muffins will not rise.
- Additions – You could easily add spinach, kale, cilantro, parsley, frozen cauliflower rice, jalapeños, etc. to this recipe!

More Healthy Egg Muffin Recipes
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Quinoa Salsa Egg Muffins
Quinoa Salsa Egg Muffins are a simple protein packed breakfast loaded with flavor and spice for an easy breakfast you can meal prep and take with you on the go!

Ingredients
- 1 1/2 cup Quinoa cooked
- 6 Egg whites
- 2 Egg Yolks
- 1 tsp Cumin
- 1 tbsp 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!
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.
Recipe Notes
- For the salsa, use one that is thin instead of chunky for best results with baking.
- My Amazon shop has more products similar to those used for this recipe and that I recommend to my nutrition clients.
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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.
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 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!
Oooooh I love this as I LOVE ME SOME ALL THINGS EB EGGS 🙂
Thanks Carla, EG eggs are the best!
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.
Great recipe Megan! Can’t wait to try it. 🙂
Thanks Daisy, happy new year!
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!
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!
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 the addition of quinoa in these! Extra nutrition and extra yum!
Lots of extra goodness. Thanks for linking my oatmeal too!
I definitely eat breakfast!!! LOVE IT! These look great & I love quinoa!!!
My favorite meal of the day!
Sounds like a delicious and easy breakfast recipe. Although at 65 calories a pop, I may need all 6 to fill me up for one breakfast meals!
Haha, yes! I usually eat one and a protein shake.
I’m huge on protein at breakfast. This recipe looks awesome! I am doing a nutrition challenge for new year’s and we’re going to be focusing on protein at breakfast soon. I’d love to mention this recipe!
I would love it if you included it. I hope you’re recovering well Sam!
I have always been a big breakfast person, and I love the sound of these grab-and-go muffins. Eggs are the GREATEST food, so good work incorporating them here! 🙂
I agree! I keep forgetting I’ve been wanting to eat them for lunch. That was inspired by you Ashley!
I’ve loving quinoa for breakfast lately. Awesome idea to bake it into a muffin! There’s not enough egg in the world for me these days.
You’ll have to try it! Hey, did you ever make it to AZ last week?
I need to get myself some quinoa solely for these muffins. YUM!!
p.s. Happy New Year! I pray that you have an amazing year full of healing, accomplishment & fun!
Thanks, happy new year to you too Jessie! I think about you and those precious girls all the time. I’m glad to see you back! xoxo
So, so YUM. I love egg dishes that can be made in advance for quick mornings. This sounds PERFECT with the addition of quinoa. Protein powerhouse! 🙂
Thanks Blair! Egg muffins are my loves.
Brilliant idea!!!! Just shared on our facebook page for our personal trainers!!
Why do you add the salsa after the muffins are in the pan? Why not mix it in with the eggs before you put them in the pan? Trying to save a step…
Definetly making these!
If you mix into the full batter, only a couple muffins with get salsa because it will fall to the bottom of the batter. I tried it both ways, and adding it to each muffin to the pan works best.
Thanks!
Mine got all stuck to the muffin pan, I put coco oil but still didn’t work. I lost half of the batter.
Oh no! You have to spray with nonstick cooking spray or they will stick just like any muffin would. Coconut oil will not work.
Hey, can I use three whole eggs so I don’t waste the yolks? Thanks!
I’m sure you could use whole eggs. Keep in mind you may get more eggs and the nutritional value will be different.
So glad I ran across this recipe on Instagram! I am putting this into my weekly prep for next week. I really want to try this with the harissa salsa from Trader Joe’s but it is a bit chunky. Maybe I can stick it in a blender to thin it down?
I’m thinking it would be fine even if it were chunky. Some of my homemade salsas have chunks of tomatoes in them and I’ve never had an issue, but blending would work too!