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Healthy Quinoa Muffins: 3 Ways

These quinoa muffins are super healthy and make the perfect breakfast treat. In this post, we also show you three different delicious flavor options.

This morning we’re having muffins. But not just any muffins. These are super-duper healthy, with no oil, no dairy, no gluten, quinoa muffins. And I’m showing you how to make them in three different flavors!

It took me a few tries to really nail this recipe down. Granted, I was being just a weensy bit picky, but I wanted them to be perfect. They had to taste great as is (with no added ingredients), but also be basic enough that you could really add whatever you wanted to use to spice them up.

Personally, I’m a big fan of recipes that have multiple uses. Pancakes are a great example. As long as you have your base recipe, you can change them up by adding blueberries or chocolate chips or chunks of banana, and it completely changes the flavor.

These quinoa muffins are exactly like that.

Gluten-Free Quinoa Muffins - in three different flavors!

All we have to do is make our basic muffin batter which is just oats, quinoa flakes, a touch of coconut sugar and some baking powder, then add in our wet ingredients which is applesauce, non-dairy milk and eggs. That’s it.

Now you could stop here and bake these babies up for a tasty morning treat, but I think at this point it’s time to have a little fun, don’t you?

Gluten-Free Quinoa Muffins - in three different flavors!

I couldn’t decide what flavors I was craving, so instead of just making one, I decided to share three:

  1. Blueberry Lemon
  2. Carrot Cake
  3. Coconut Chocolate Chip

The blueberry lemon is a fresh twist on a classic muffin and I’m crazy for it. With that burst of citrus flavor or the mini blueberries sprinkled throughout, they’re the perfect morning treat.

The carrot cake ones are equally as delicious, but just a tad heavier. Since I’m a big carrot fan, I might have gone a little crazy with the shredded carrots, so I think if I had added just a bit less, they would have been a lot lighter. I also added walnuts to these babies because I’m all about the nuts in my carrot cake. Oh and these would also be delicious with a quick vegan cream cheese frosting!

The final flavor and arguably my favorite (no surprise here) is the coconut chocolate chip. Like SO good. I used flaked coconut which I’m obsessed with and dark chocolate chips which gave the whole muffins a dessert-like taste. BUT they’re also totally healthy enough for breakfast! (<– yes my chocolate for breakfast obsession continues…anyone else? should we maybe start a hashtag?) Moving on…

Healthy Quinoa Muffins made without fat, gluten or dairy - shown in 3 different flavors!

Another quick note about these muffins before we dive into the recipe: they might be a little less sweet than the recipes you are used to. I did this purposely because I think a) you can make them more sweet with your add-in choices and b) starting your day with a sugar-loaded baked good is not going to get you off on the right foot. Blood sugar crash much?

So here are just a few tips to amp up the sweetness if your little heart desires that:

  1. Add a dash of stevia. This won’t increase the calories or sugar content at all, but it will make the muffins taste sweeter. You can use powdered (just a sprinkle) or liquid (only a few drops).
  2. Swap banana for the applesauce. The applesauce in this recipe is unsweetened, so if you want to keep them healthy, I think the best bet is to use bananas instead of the applesauce. Bananas have more natural sugars in them BUT they’re also a different consistency. You might find that you need to add a few more tablespoons of milk to get the right consistency. You could also follow my skinny banana chocolate chip muffins as your base.

Those two things should do it, but I really think you should make them first and see how they taste. I loved them as is – especially with the chocolate chips and fresh berries. So yum!

Skinny Quinoa Muffins: 3 Ways

5 from 2 votes
All we have to do is make our basic muffin batter which is just oats, quinoa flakes, a touch of coconut sugar and some baking powder, then add in our wet ingredients which is applesauce, non-dairy milk and eggs. That’s it.
author: Alyssa
yield: 9 muffins
Healthy Quinoa Muffins made without fat, gluten or dairy - shown in 3 different flavors!
Prep: 15 minutes
Cook: 12 minutes
Total: 27 minutes


for the base recipe:

flavor option 1: lemon blueberry

  • 1/2 cup - 1 cup blueberries
  • Zest of 1 lemon

flavor option 2: carrot cake

flavor option 3: coconut chocolate chip


  • In a large mixing bowl, whisk together the flour, quinoa flakes, oats, sugar, baking powder and salt. Set aside.
  • Beat together the wet ingredients in a separate mixing bowl. Add to the dry and mix to combine. The consistency should be that of a runny oatmeal. Let the batter stand while you preheat the oven to 375 degrees F. If by the time the oven is ready the batter seems too thick (you should be able to still stir it easily) add more milk 1 tablespoon at a time.
  • Just before baking, folding in your desired add-ins.
  • Spray a muffin tin with nonstick spray and fill the wells 2/3 of the way full. Bake on the center rack for 12 - 14 minutes until muffins are starting to brown and no longer soft to the touch.
  • Remove and let cool in the pan for 3 - 5 minutes then transfer to a wire rack and cool completely.
  • Enjoy!


1) You can make your own oat flour by simply grinding gluten-free rolled oats in a high-powered blender until they resemble a fine powder.
2) The add-in measurements are for the full recipe. Scale it down proportionally if you want to make different flavors from one batter.


Serving: 1muffin | Calories: 134.69kcal | Carbohydrates: 22.91g | Protein: 4.7g | Fat: 2.91g | Saturated Fat: 0.55g | Cholesterol: 18.19mg | Sodium: 91.99mg | Potassium: 225.07mg | Fiber: 2.02g | Sugar: 4.61g | Vitamin A: 77.93IU | Vitamin C: 1.08mg | Calcium: 73.52mg | Iron: 1.3mg
cuisine: American
course: Snack

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39 comments on “Healthy Quinoa Muffins: 3 Ways”

  1. Hello there, excited to try these… They are in the oven now. Wondering where you got for 240 for the calories for one muffin. I just did the math and it’s closer to about 115. Maybe because I use quinoa powder instead of quinoa flakes? Thx!

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    Micayla Vranic

    Yummy! My friend and I are going to make these these tomorrow night, so excited, I’ve been searching for a good quinoa muffin recipe!

  3. Pingback: Meal Prep & Fridge Organisation | crosstitchery

  4. i hope you are in the works in making a quinoa cookbook, i would buy :):):):):) lol love your recipes, and thank you for sharing.

  5. I like them all! It is just great to be able to change about without too much fuss. When I do this I have one big bowl,for the mix and three others in front, I generally add ginger to one, cinnamon to another and almonds or cashews or walnuts to the other. I have been known to slip a 4th one in and that has a good do.lop of cacao powder. Something for every one and every mood.
    I like savoury ones is there the same sort of playing around I can do for a good chile one, a broccoli and nutritional yeast and a fried onion and leek one? They are current favourites. I like a curry type if you slip in a fourth!

  6. I do like the odd sweet thing, just now and then…. Have you got a neutral, goes either way then or a real,savoury one? I love those.

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    Susan S. Bradley

    Foundation recipes are so practical. Love the variations you included here. Blueberries aren’t in yet, so I’ll try the coconut-chocolate chip version first. 🙂

  8. I’d have to try all 3 in order to make an informed and responsible decision as to which one I love most! 😉

  9. These muffins look fantastic! I love how you can throw just about anything you want into these little gems. I’m all about chocolate and coconut 🙂

    1. Hi Sarah! It’s just about the same measurements I find. But I tend to blend extra so I have it one hand. It goes well in so many recipes!

  10. Do you have any ideas what I can use instead of oats for celiacs who are not allowed oats (even certified GF ones)? thanks! Brigitte

    1. Hi Brigitte! I *think* you could try using a GF flour, just using a little less. I’d say like a cup of flour maybe? Since the GF flour is a lot lighter you probably won’t need as much regular flour. If it seems too wet, then keep adding flour 1 tablespoon at a time until you get the right consistency. I haven’t tried this so I can’t be sure if it will work, but it’s worth a shot! Let me know how it goes 🙂

  11. These muffins look amazing!! Cannot wait to try. Can anyone recommend an egg replacement for these muffins? Thanks:)

    1. I think you could probably try it with a flax egg, but I’m not sure they would rise as much. I say give it shot!

  12. Love the varieties of ingredients you showcase here! I make baked goods each weekend for my husband to take to work on Mondays, and this is a great variation on the things I regularly make/send. Can’t wait to give these little gems a try!

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    Jessica @ Nutritioulicious

    I love this! All 3 of those muffins look and sound delicious, but my favorite is the blueberry lemon. And I’m so glad you used applesauce instead of bananas 😉

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    Kacey @ The Cookie Writer

    Woohoo! Gluten-free muffins for my mother-in-law! Cannot wait to experiment with them! She eats the same things over and over again.

    1. Haha I’m totally the same way. Good thing I’m a food blogger because it forces me to eat different stuff all the time 😉 Let me know how they work!

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    Christine Pittman

    I love that there are a variety of ways to make these muffins. It helps prevent boredom, and gives me a reason to make them several times in a row.