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Home » Recipes » Healthy Muffin Recipes

Apple Cinnamon Quinoa Breakfast Muffins

By: Kathryn Doherty | Last Updated: Mar 6, 2025 | Published: Jan 8, 2016
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Apple cinnamon quinoa breakfast muffins are wholesome mini muffins loaded with quinoa, oats and apples! They're great finger food for little ones and a lovely, portable, pop-able breakfast or snack for older kids and adults!

Close up of a trio of mini muffins made with apple and quinoa on a small white plate.


 

I've got a fun breakfast treat for you today!

We eat a lot of oats around here, especially for breakfast. Overnight oatmeal jars are a weekly staple and have tons of healthy oatmeal recipes.

But I also like to try and branch out to other grains from time to time. Variety is good, and I want to expose my kids to different types of wholesome foods.

These apple cinnamon quinoa breakfast muffins are perfect! Okay, yes, they also have oats, so I’m not straying too far I realize.

But it’s a great way to get a different grain in at breakfast time - quinoa at that! - along with some familiar and popular apple and cinnamon flavors.

And yes, quinoa is technically not a grain. It’s a seed. Details, details, details.

Apple cinnamon quinoa bites stacked

These little mini muffins are soft and full of apple and cinnamon flavor with a perfect amount of sweetness from the maple syrup. (Yay for naturally sweetened!)

They’re also gluten-free (make sure you use certified gluten-free oats) and you could sub a couple of flax eggs for the eggs if you want to make them vegan.

Quinoa is protein packed, and you've got the oats and fruit, so these really are a pretty well-rounded little meal or snack all on their own. Sorta ticks all the boxes.

Plus, I love that they store so well, too.

I make a big batch, we eat a bunch the next day (they're great both warmed up and cold from the fridge) and I freeze the rest to pull out for another morning. Super simple!

My kids eat these for breakfast or morning snack and I like that I can grab a couple to go if I’m on the run since they are so portable.

They’d even be great to send for school lunches.

Three mini apple cinnamon quinoa muffins with sliced apples to the side on a small white plate.

Now, I've got a few quick notes and substitutions coming up on how to make quinoa breakfast muffins. Just tryin’ to be helpful.

If you want to jump on down to the recipe, simply scroll right on through the rest of the text. The recipe card is near the bottom of the page, above the comments section.

Ingredient Notes:

  • Quinoa: The quinoa needs to be already cooked for this recipe, so please plan accordingly.
  • Oats: The oats on the other hand are uncooked and raw. I use regular old-fashioned rolled oats, but quick oats would be fine to use here, too.
  • Maple syrup: Be sure to use pure maple syrup. Or swap it out for the same amount of honey if you'd rather.
  • Eggs: As mentioned, you can replace the eggs in this recipe for flax eggs if you need this recipe to be vegan.
  • Apple: Use your favorite variety of sweet apple, like Fuji or Gala.
A hand holding up an apple quinoa mini muffin.

Oh, and in case you are in the market, I use and love this mini muffin tin. These pancake mini muffins are on regular rotation in my house and you can also make baked donut holes in mini muffin tins.

As mentioned, these quinoa breakfast muffins store great, so you can definitely make a batch ahead for the week.

Leftovers, once cooled, can be stored in a covered container in the refrigerator for up to 5 days. Or freeze the leftover mini muffins in a freezer-safe bag for up to 3-4 months.

Make your mornings a little easier and healthier this year with these quinoa breakfast bites.

Enjoy!

XO,

Kathryn

P.S. Check out my other healthy muffin recipes for more inspiration.

Close up of a trio of mini muffins made with apple and quinoa on a small white plate.
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3.93 from 171 votes

Apple Cinnamon Quinoa Breakfast Muffins

Apple cinnamon quinoa breakfast muffins are wholesome mini muffins loaded with quinoa, oats and apples! They're great finger food for little ones and a lovely, portable, pop-able breakfast or snack for older kids and adults!
Prep Time10 minutes mins
Cook Time15 minutes mins
Total Time25 minutes mins
Yield: 20 mini muffins

Ingredients

  • 1 cup cooked quinoa
  • 1 cup old fashioned rolled oats
  • 1 teaspoon ground cinnamon
  • ¼ teaspoon salt
  • 2 large eggs, lightly beaten
  • ¼ cup maple syrup
  • 1 teaspoon vanilla extract
  • 1 cup finely chopped apples

Instructions

  • Preheat the oven to 350. Spray a mini-muffin tin with cooking spray.
  • Mix quinoa, oats, cinnamon and salt together in a large bowl.
  • Separately, beat the eggs in a small bowl. Stir in maple syrup.
  • Add the egg mixture to the quinoa mixture and stir to combine. Fold in the apple pieces.
  • Fill each mini-muffin cup all the way full. Use your spoon to pack each one down a little bit.
  • Bake at 350 for 15-20 minutes.

Notes

Quinoa: The quinoa needs to be already cooked for this recipe, so please plan accordingly.
Oats: The oats on the other hand are uncooked and raw. I use regular old-fashioned rolled oats, but quick oats would be fine to use here, too.
Maple syrup: Be sure to use pure maple syrup. Or swap it out for the same amount of honey if you'd rather.
Eggs: As mentioned, you can replace the eggs in this recipe for flax eggs if you need this recipe to be vegan.
Apple: Use your favorite variety of sweet apple, like Fuji or Gala.
Leftovers: Store the mini muffins in an airtight container in the fridge for up to 5 days. Or freeze the extras in a freezer bag for up to 3-4 months.

Nutrition

Serving: 2mini muffins | Calories: 96kcal | Carbohydrates: 17g | Protein: 3g | Fat: 2g | Polyunsaturated Fat: 1g | Cholesterol: 37mg | Sodium: 70mg | Fiber: 2g | Sugar: 6g
Tried this recipe?Leave a comment below or follow me on Instagram @familyfoodonthetable and tag me in your photo!
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Reader Interactions

Comments

  1. Mahy

    January 08, 2016 at 10:48 pm

    These look great! I am so in the mood for anything apple cinnamon right now! Will try these soon:)

    Reply
    • Kathryn

      January 10, 2016 at 8:36 am

      Can't beat that apple + cinnamon combo, right?! Hope you love these little muffins!

      Reply
      • Amy

        March 13, 2016 at 9:46 pm

        Do you have the nutrition info. on these muffins?

        Reply
        • Kathryn

          March 14, 2016 at 9:26 am

          Hi Amy! I currently don't include nutrition information for my recipes, but you could plug this into an online nutrition calculator, like this one: http://www.myfitnesspal.com/recipe/calculator. Hope that helps!

          Reply
  2. Lisa @ Chocolate Meets Strawberry

    January 09, 2016 at 6:18 am

    Kathryn, these look absolutely fantastic!! I've just pinned them as I definitely want to make some. I've been looking for a quick breakfast option lately (I'm back at work this coming week after a long break over Christmas and feel like I might be just a little slow come 5am when the alarm goes off...), and these fit the bill perfectly - high in fibre, low in sugars, no refined sugar at all and super simple. I will let you know how I go! Thank you so much for the recipe 🙂 On a side note, it's interesting that quinoa is actually a seed. I've heard that before somewhere I'm sure, but I always forget it! Kind of like I forget that tomatoes are a fruit! As you said - details, details, details. I guess we're expected to know these things as food bloggers, right? 😉

    Reply
    • Kathryn

      January 10, 2016 at 8:38 am

      Haha, right Lisa! I'm like you in that I pick up tid-bits here and there from cooking and from my job as a health and nutrition editor. Some of it sticks and some of it doesn't... 😉 And a big YES to easy, fast, healthy breakfast options for those early mornings when everyone's hungry and everyone's busy! I hope you love these!

      Reply
  3. Rachel @ Bakerita

    January 10, 2016 at 9:29 am

    These apple cinnamon breakfast muffins look fabulous and so nutritious! I adore anything with apple and cinnamon, so these must make an appearance in my kitchen soon!

    Reply
    • Kathryn

      January 10, 2016 at 2:54 pm

      Thanks Rachel! It's such a delicious combo, right? I hope you give these a try and enjoy them!

      Reply
  4. Lauren @ Create Bake Make

    January 14, 2016 at 7:13 pm

    Oh these look fabulous, I'd love to start my day with a couple!

    Reply
    • Kathryn

      January 14, 2016 at 9:49 pm

      At least 2... probably 3. Maybe 4... Have a great weekend, Lauren!

      Reply
  5. aimee @ like mother like daughter

    January 16, 2016 at 10:42 pm

    I've been wanting to add more quinoa to my repetoire, so I can't wait to try these out! I love apple cinnamon and just know my little guy would love these for breakfast or a snack!

    Reply
    • Kathryn

      January 17, 2016 at 7:27 pm

      I'm with you - always looking for new ways to incorporate quinoa 🙂 Hope you both love these mini muffins!

      Reply
  6. Karly

    January 19, 2016 at 9:29 am

    I LOVE this muffin idea! Thanks for linking up with What's Cookin' Wednesday!

    Reply
    • Kathryn

      January 19, 2016 at 1:28 pm

      Thanks Karly! They are a big hit at our house 🙂

      Reply
  7. Frugal Hausfrau

    January 20, 2016 at 12:33 am

    This is going on my must make list!! I love these healthy muffins!

    Thanks for linking up with us on Throwback Thursday - we appreciate it, and are always looking forward to next week's posts, too!! 🙂 Be sure to follow our pinterest board, too! 🙂

    Mollie

    Reply
    • Kathryn

      January 20, 2016 at 5:53 am

      Thanks! They are a great little morning treat - or even afternoon snack! And thanks for hosting such a yummy party each week 🙂

      Reply
  8. Anita

    January 22, 2016 at 1:37 am

    This recipe looks so delicious! Hi, I'm Anita visiting from Foodie FriDIY.

    Reply
    • Kathryn

      January 22, 2016 at 8:32 pm

      Thanks Anita!

      Reply
  9. Kristy Alexander

    October 03, 2016 at 8:31 am

    In what liquid do you cook the quinoa to have it ready to go in these muffins? In water?

    Reply
    • Kathryn

      October 03, 2016 at 9:31 am

      Hi Kristy! Yes, I use water to cook the quinoa. Hope you give these a try!

      Reply
  10. Elise

    March 13, 2017 at 4:32 pm

    I made these muffins yesterday and was quite disappointed with how they turned out. They are super crumbly and very plain. Smell really good though!

    Reply
    • Kathryn

      March 13, 2017 at 8:32 pm

      Hi Elise - I'm sorry to hear they didn't work for you! I've made these multiple times and they've never been crumbly for me. I do let them cool first so they set up; I wonder if that was the problem. Also, yes, they are not super sweet since they're meant to be a healthier breakfast muffin. But you could certainly add some more maple syrup or serve them with a spread of fruit jam if you'd like!

      Reply
  11. Diane

    May 05, 2017 at 9:35 am

    Would it work to make these as a full size muffin? 8 don't have a mini muffin pan.

    Reply
    • Kathryn

      May 06, 2017 at 8:31 am

      Hi Diane! Sure, I think that would work. You'll just need to bake them for a bit longer. I'd suggest checking them around 22-25 minutes and seeing if they seem done.

      Reply
  12. Caitie

    May 26, 2017 at 2:19 am

    This is an amazing recipe!! All of my family tried some & they loved it too! I also made some with mixed berries instead of apples, & some with apples & mixed berries combined, & they tasted Amazing as well!! They r super fast to make and taste delicious! Definitely try this one out 🙂

    Reply
    • Kathryn

      May 26, 2017 at 10:34 am

      Hi Caitie! I'm so happy to hear you loved these muffins! Thanks so much for letting me know - and have a wonderful weekend! 😊

      Reply
  13. Shannon

    July 01, 2017 at 4:34 pm

    I just made these and they are so "neat"!! I was going to do the regular size muffin pan, but I'm glad I did the mini, they are perfect bites! Ive already ate like 6 of them! I used honey, they are not sweet, they are just yummy and I can't wait to have some with some good greek yogurt! Thanks!

    Reply
    • Kathryn

      July 02, 2017 at 10:50 pm

      I'm so, so happy to hear that Shannon! Thanks so much for sharing!

      Reply
  14. Shannon

    July 08, 2017 at 11:39 am

    These were sooooo good!!! What a great combo! I'm so glad I found your site and this recipe. Thank you for sharing. So easy and delicious! Very versatile..... I'm memorizing this!! Keep up the good work!

    Reply
    • Kathryn

      July 09, 2017 at 3:29 pm

      I'm so happy to hear you loved them Shannon! Thanks so much for sharing! 😊

      Reply
  15. Amy

    July 26, 2017 at 3:31 pm

    Hey- these look great. I am allergic to oats, have you ever made a quinoa muffin without grains or any ideas for a substitute?
    Thanks,
    Amy

    Reply
    • Kathryn

      July 26, 2017 at 8:32 pm

      Hi Amy! We are oats-crazy in my house so I've never looked for a substitution. However, I just did a bit of poking around and some people have suggested using ground flax, rice bran, quinoa flakes or chia seeds in place of oats when baking. I haven't tried it myself but hopefully that gives you some options to try!

      Reply
  16. Desi

    August 27, 2018 at 4:19 pm

    Loved these little bites! Really good with a small smear of homemade apple butter....

    Reply
    • Kathryn

      August 28, 2018 at 4:27 pm

      Now that's a great combo! So happy to hear you enjoyed the muffins! 😊

      Reply
  17. Stephanie Silva

    January 17, 2019 at 5:08 pm

    Would these work with flax eggs?

    Reply
    • Kathryn

      January 18, 2019 at 8:09 am

      Hi Stephanie! I haven't made this recipe with flax eggs, but I think it should work fine. Would love to hear if you try it!

      Reply
  18. Tara

    June 25, 2020 at 2:09 pm

    These taste great, but I made 6 regular size, at 20 minutes they crumbled and don’t retain shape? How long should I cook them?

    Reply
    • Kathryn Doherty

      June 29, 2020 at 11:52 am

      I'm not sure this will work for regular size muffins. Using the small mini muffin pan and packing the mixture into them is the way they get set up. I think you'd have to adjust the recipe to have more binder to make it work for a regular size muffin.

      Reply
  19. Emily Forsmark

    February 20, 2021 at 1:49 pm

    I was curious how you only got 10 muffins. I got 24 mini muffins and 2 normal sized ones. Also, the mixture was very wet. Should it have been.?

    Reply
    • Kathryn Doherty

      February 21, 2021 at 9:51 am

      Hi Emily! The yield in the recipe card says 20 mini muffins, not 10. I fill and then pack mine down in the mini muffin tin so they will stay together better, which may mean I got fewer, depending on how you did yours. And the mixture really shouldn't be very wet; there's hardly any liquid.

      Reply
  20. Emily Forsmark

    February 21, 2021 at 10:36 am

    The nutrients information says it yields 10. Mine turned out good. Not crumbly at all. I used real maple syrup vs imitation...don't know if that made it wetter or not. Still good though. I would make again.

    Reply
    • Kathryn Doherty

      February 21, 2021 at 11:45 am

      Ah, OK, the serving size is 2 mini muffins so 10 total servings. (Though my kids often eat 3-4 in a sitting.) And I only ever use real maple syrup, too, but so many factors can affect a batter. So glad they turned out well for you and you liked them! 😊

      Reply
3.93 from 171 votes (171 ratings without comment)

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Hi there! I’m Kathryn Doherty, a cookbook author, mom of two, and devoted food and home cooking nut. I’ve got lots of easy recipes to help you get delicious food on the table for your family!

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