Apple-Pecan Quinoa Muffins


I am in love…but my husband need not be concerned.  There is no love triangle that would threaten to take me away from him; in fact, he’s been quite happy with my newfound adoration…for quinoa.

In the past, this South American seed (considered to be an ancient grain) would be served in my kitchen only once every several months but lately I’ve found myself trying to add it to everything I can.  I can’t quite account for this change but I must admit I’ve been enjoying its versatility, allowing me to use it as a savory cake, in a salad and now in a baked good.  I can confidently say:  quinoa is here to stay.



When a friend gave me a large bag of apples from her tree recently I knew I would be baking with them but I wanted to make something other than a tart or galette, since I’ve shared quite a few of them here already.  We had another friend staying with us, too, and between him and my husband I couldn’t keep up with demand for bread to help fuel them for their morning bike rides.  I baked Irish brown bread but that only lasted a couple of mornings so I decided to bake muffins one afternoon and of course I knew that quinoa would be making an appearance here, too.



Besides the apples and quinoa being the foundation of these muffins I also spotted a couple of bags of Trader Joe’s candied pecans in the pantry.  I consider the latter a convenience item and add them to salads for a sweet-salty crunch.  Why not add them to the muffins, I thought.

Well, that turned out to be a good decision.  We all loved these muffins and couldn’t get enough of them.  Not greasy but moist, the apple chunks lending freshness, the pecans some crunch, the cinnamon some depth–we inhaled these muffins.  I didn’t use much sugar in the batter so don’t expect a lot of sweetness here but the best part?  The quinoa added such a nice texture–almost like cornmeal–that I can’t wait to bake with it again.  Savory quinoa muffins maybe?

** Substituting the apples and pecans for other fruit and nuts, as well as substituting the whole wheat flour for gluten-free flour, this would make a great base recipe for other flavor combinations.   



4.6 from 14 reviews
Apple-Pecan Quinoa Muffins
Forget greasy muffins. These muffins are packed with apples and pecans and healthy, too.
Serves: Makes 12 muffins
  • 1 cup whole wheat flour (or your flour of choice)
  • 1 cup cooked quinoa
  • ½ cup lightly-packed brown sugar
  • 2 teaspoons baking soda
  • ½ teaspoon salt
  • 2 teaspoons cinnamon
  • ¼ cup vegetable oil
  • 1 egg
  • ⅔ cup milk (I used nonfat)
  • 1 cup chopped apples (about ½ large)
  • ½ cup chopped pecans (I used candied pecans for more flavor)
  1. Preheat your oven to 400°F. Lightly grease a 12-muffin tin (or use cupcake liners; I used a ⅓ cup muffin tin) and set aside.
  2. Whisk together the flour, brown sugar, salt, cinnamon and baking soda in a large bowl then stir in the cooked quinoa.
  3. In a separate bowl combine the oil, milk and egg then stir into the dry ingredients.
  4. Fold in the apples and pecans and spoon the batter into the muffin tin.
  5. Bake for 18-20 minutes or until golden brown. Cool on a wire rack before serving.
Substituting the apples and pecans for other fruit and nuts, as well as substituting the whole wheat flour for gluten-free flour, this would make a good base for other flavor combinations.



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  1. Amazing photos!

  2. What gorgeous apples – do you know what variety they are? These muffins look like the perfect use for them – I love your candied pecan addition!

    • lemonsandanchovies says:

      Laura, my friend doesn’t know what kind they are. They’re slightly tart with a dry texture, really crisp–so good!

      Glad you like the muffins! 🙂

  3. What a delightful, healthy muffin! A must try! Gorgeous photos!!!

  4. They look so healthy I can feel myself glowing with health already. There are times when cupcakes must be put aside to be replaced by good down-to-earth food.

  5. Jean – it is so wonderful that you have found such an adoration for quinoa! These muffins look fantastic and I must make these soon. Love all of the photos – just stunning. BTW – Fridge arriving next Friday – YEAH!

  6. Dang! This looks sooooooo good! I bet they taste sooooooooo good as well! Apples and pecans are one of my fave muffin ingredients. The addition of quinoa just elevated the healthy factor of these muffins! Yay, bookmarking for future use.

  7. What a great and pretty healthy muffin. I too am loving putting quinoa in things. I put quinoa in some meatball type things awhile ago (never blogged about it), and it was amazing!

  8. Great job on incorporating quinoa in a muffin that boost the nutrition up for sure. Your photos are so beautiful and how lucky to get a big bag of home grown apples. Is applesauce in the works yet?

  9. Beautiful photos Jean! I love that you’ve added cooked quinoa to your apple pecan muffins-I have to give it a try too;-) The first time I made quinoa, i thought it’s cute- the way it puffs up and gets those little tails! The fact that it tastes good and is healthy- all the better!

  10. beautiful post!!!
    And such healthy muffins….
    I need to start using more Quinoa… This recipe looks fabulous… Will sure give it a try!!!

  11. Just tried this recipe out with the wife’s help and I must say they are superb! Thanks for posting it!

    • lemonsandanchovies says:

      Rich, a very, very late thank you but I’m so glad you tried my recipe and you liked it. Thanks so much for taking the time to give me feedback! 🙂

  12. Hi Jean,
    Your muffins look so gorgeous and the colours scream autumn. I too love quinoa but have yet to bake with it. Can’t wait to give this a try. Thanks for sharing. Hope you are well:)

    • lemonsandanchovies says:

      Hi, Nancy! All is well–just been crazy busy. Glad you liked these muffins–it’s been surprisingly fun working with quinoa. Hope you’re well, too. 🙂

  13. What a wholesome healthy muffin – perfect for a back-to-school breakfast.

  14. I smile at your current quinoa obsession 😉 Beautiful photos, Jean – you have a great eye for composition and color. Happy anniversary!

    • lemonsandanchovies says:

      Priscilla, that’s so sweet, thank you. 🙂 I’ve been smiling since reading your generous compliment. 🙂

  15. Melissa White says:

    I also have an obsession with quinoa and make a breakfast cereal cooking it along with apples, cranberries & toasted pecans. I’m definitely going to make this recipe, using gluten-free flour (probably involving almond flour or coconut flour). Can’t wait to see how they come out. Thanks!

  16. I love using quinoa in baking too. I wasn’t sure how it would go at first, but it’s fantastic. I especially love using flaked quinoa in crumbles.

    I have to say I’m in love with that apple photo. It’s simply stunning!

  17. These muffins sound fantastic! Apples paired with pecans and cinnamon is divine…add the texture of quinoa and I’m sure they are out-of-this-world! Stunning photos too, Jean!

  18. Hmmm healthy and delicious muffins, Jean! I have never tried muffins with quinoa before (obviously I have to make it on my own) since I don’t think store sells it. Apple and pecan sounds great in these muffins! I truly love your styling and shot on these muffins!

  19. Hi Honey!!
    I, too, love quinoa! But I never thought to put it in a muffin…excellent idea!
    And your photos…my oh my…loooove ’em!

  20. The apples, the quinoa, the candied pecans- they all sound so good in this delicious, yet healthy muffin. I have some quinoa at home and never thought to bake with it. Thanks for the lovely advice.

  21. Gorgeous pictures!!! These look so healthy and filling!

  22. Love the idea of using quinoa in a muffin, Jean! These muffins will definitely be added to the baking rotation very soon – I am positive that the family will love it – and it will also be perfect to toss into lunches once school begins.

  23. Lora @cakeduchess says:

    I’m so ready to get baking with apples. These apples are gorgeous! Your photo styling has me ready for fall and cooler days. These are great for the kids as an after school snack (and for me too!):)

  24. These were so good! LOVE them and I calculated they were about 149 cal each 🙂 I did them with mixed nuts .

    • lemonsandanchovies says:

      Mia, thanks so much for trying these muffins. So glad you liked them and thanks for the calorie calculation–I never do that and it’s so nice to have that number for these muffins. 🙂

  25. Such a beautiful post with a cooling reminder that Fall is on it’s way 🙂 Lovely muffins as well as photos…a delight!

  26. Beautiful muffins! Love the idea of baking with quinoa!

  27. Well I must admit I do not write comments and this is my first. I am sorry to say I just made these muffins and followed the recipe carefully they looked great but tasted horrible. All I can taste is a nasty after taste of the baking soda. Not sure why? Can anyone suggest a different method with out so much baking soda.
    For those who love Quinoa I cook a recipe from the net called Vegetarian Stuffed Peppers which include Quinao, they are super delish!

    • lemonsandanchovies says:

      Hi, Lynda. Thanks for your feedback and I’m disappointed that the recipe didn’t work out for you. I didn’t notice that about the baking soda but I’ll see when I make these again. The recipe has garnered lots of positive feedback so I’m not sure how things went wrong. Maybe a reader will be able to offer suggestions on how to approach this next time. Thanks again for taking the time to submit a comment.

      • I know Lynda’s comment was posted almost a year ago, but one possible reason for the baking soda taste is that Lynda’s apples weren’t tart enough.

    • I loved these muffins as well! I used the cooked quinoa and didn’t have the flour so used whole wheat pastry flour. I also used coconut oil in place of the veg oil. They turned out great! I think my kids thought they should be a tad sweeter, so I might add a bit more sugar for them next time. However, I had the same problem as someone mentioned above about the baking soda taste. I still rate this recipe very highly because it was just that one problem. I’m wondering if I could use less baking soda or maybe baking powder in its place. not sure about converting the amounts. If anyone has suggestions, please let me know. I plan for this to be my go-to muffin! This will work well with any type of add-ins!

  28. Hi
    The recipe looks great – is there something natural i can substitute for the brown sugar? (stevia?) I am on an anti candida diet.

    • lemonsandanchovies says:

      Gee, Jason. I wish I knew. I have never used sugar substitutes before. I hear of other bakers using Stevia but I’m not familiar with conversions. If I find something I’ll let you know. Thanks so much for your interest in this recipe.

  29. Umm OMG these are the best muffins I’ve ever made. The only thing I did different was added a little extra apple and added some raisons too. Thanks so much for posting this, I’ve just discovered Quinoa and the health benefits so have been searching recipes, boy did I pick the right one! I’m going to share with my vegetarian neighbours but it will be hard to part with them! I will definitely be making these again and again!

    • lemonsandanchovies says:

      Angie, I’m so glad you liked these muffins, yay! I like the modifications you made–the more apples the better and I like raisins, too. Thanks so much for taking the time to give me feedback! 🙂

  30. Success!! My family of four destroyed an entire dozen!!! My children, (ages 6&4,) ate more than my husband and I ate! Thank you so much for this great recipe.

  31. Delicious! I’ve been looking for high-protein muffin recipes for breakfast, and I was especially interested in trying a muffin with quinoa. I made this recipe with quinoa flour, as it adds more protein and is gluten-free. I thought this might give the muffins too strong of a quinoa flavor, but it didn’t. I also used almond milk instead of regular milk, added a teaspoon of vanilla, and used candied pecans and one large Granny Smith apple. I was a little surprised at the 400-degree baking temp, which seemed high, but the muffins were done after exactly 18 minutes, and they had some nice yummy crispy edges. Oh, and I was out of baking soda so I used baking powder instead. I wasn’t sure if one could be substituted for the other, but the result was a surprisingly delicious and nutritious muffin. Thank you!

  32. I’ve made these muffins many times and everyone loves them! Just made them again and they stuck to the baking cups for the first time! Any idea why this happens?

    • lemonsandanchovies says:

      Sarah, so glad you like these muffins. I don’t know what would have caused them to the baking cups this time; I haven’t come across that issue so far. I wish I had an answer for you. If it happens again, please let me know.

      Thanks so much for your feedback!! 🙂

  33. As Bed and Breakfast Owners/Innkeepers, we have noticed more guests looking for healthy alternatives. We have been experimenting with Quinoa, a good source of protein, iron, and fiber, quinoa is a quick and flavorful way to get in a serving of whole grains. Today guests loved your recipe for Apple-Pecan Quinoa Muffins so much that they asked for bags to take some on the plane with them. I used coconut oil vs vegetable, which is also better for you according to Dr. Oz. Thank you for sharing your recipe.

    • Colleen, what a nice comment to receive, thank you. I’m so glad you tried one of my recipes and, even better, that your guests enjoyed it. Yes, I agree that coconut oil is really good for you; I’ve been using it in recipes when I can, too. Thanks so much for the wonderful feedback! 🙂

  34. Made these this morning and they are fabulous!! But I tinkered a bit, and here’s what I did:

    -Used dried apples instead of fresh and also added a handful of dried cranberries.
    -Used coconut oil instead of vegetable oil
    -Used 1/4 Oatmeal for flour
    -Used walnuts instead of pecans
    -Sprinkled cinnamon chips atop muffins just before baking

    Texture of these muffins is incredible! Kids loved them, and I love that they have lots of protein and not much sugar. Thanks for sharing this 5 Star recipe. I’ll definitely use again!

    • Lora, I’m so glad you liked these muffins and I like your substitutions. Thanks so much for taking the time to come back to give me feedback! 🙂

  35. Hello

    Would you be able to tell me the nutrional values in the recipe for the Apple-Pecan Quinoa Muffins.
    Particularly (fat,carbs,protein & fiber).
    thanks very much.

    • Hi Evelyn, I don’t track nutritional values on my recipes. I’m guessing you can find a tool online that would provide this information. Thanks a lot for checking out the recipe! 🙂

  36. Hi, these look amazing!
    Just to clarify, is it one cup cooked quinoa oe one cup uncooked quinoa, then cooked? Please let me know, thanks!

  37. lemonsandanchovies says:

    Hi, there! It’s one cup already-cooked quinoa. 🙂 Please let me know if you have other questions. 🙂


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