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Chocolate Chip Quinoa Muffins

These muffins are an incredible treat for vegetarians (and non-vegetarians alike, especially for Lent Fridays or Meatless Mondays) because they are chock-full of protein with all that delicious quinoa. But they’re still a slightly sweet breakfast muffin that even the kids love. But beware, if you want your chips to stay chips, let your quinoa cool before mixing it in…especially if you’re out of regular chocolate chips and use minis instead…they will melt.  For this batch, I ended up with more Chocolate Quinoa Muffins with a few surviving chips. But as you all know by now, I’m no expert baker. I’m merely persistent. They taste great and aren’t cloyingly sweet, so I’m happy. If you’re not a chocolate fan, sub in raisins, cranberries or nuts.

Chocolate Chip Quinoa Muffins


Kristi @ onceamonthmeals.com, adapted from Quinoa Muffins


  • 1 cup quinoa, rinsed (~2 cups cooked)
  • 1 cup water
  • 0.25 cup applesauce (I make mine minus the sugar and plus a bit of vanilla)
  • 2 cups flour, unbleached (I used whole wheat white)
  • 0.5 cup brown sugar or sucanat, packed
  • 1.5 teaspoons baking powder
  • 1 teaspoon salt
  • 0.5 cup chocolate chips
  • 0.75 cup milk, whole
  • 1 large egg or egg substitute
  • 1 teaspoon vanilla extract


Preheat oven to 350 degrees. In a medium saucepan, bring quinoa and water to a boil. Reduce to a simmer; cover, and cook until water has been absorbed and quinoa is tender, 11 to 13 minutes.

Brush muffin pan with oil; dust with flour. In a medium bowl, whisk together flour, sugar, baking powder, salt, chocolate chips, and cooked quinoa (double the amount of uncooked, so 2 cups if you cooked 1 cup); reserve any leftover quinoa for another use.

In a small bowl, whisk together applesauce, milk, egg, and vanilla. Add milk mixture to flour mixture, and stir just until combined; divide batter among prepared muffin cups.
Bake at 350 25 to 30 minutes. Cool muffins in pan, 5 minutes; transfer to a wire rack to cool completely.

Freezing Directions:

AFTER baking and cooling, divide among freezer bags and freeze. To serve: Thaw. Reheat in microwave for 30-45 seconds.

Servings: 6 (12 muffins)

**conversion chart image provided by Erik Spiekermann


37 Responses to “Chocolate Chip Quinoa Muffins”

  1. Meredith says:

    Do you think that this would work with red quinoa? I have a box of trader joe’s red quiona on the pantry shelf waiting to be used…..

    • kristi says:

      I think that would work just fine! Your cooking time and water amount may be slightly different (as will the taste), but I think it would be good. The red quinoa has a bit earthier flavor than the regular (white) quinoa, so it’s also possible you’d want to add a touch more sugar.

  2. Robyn says:

    These look like chocolate muffins. Is there cocoa powder in it as well?

    • kristi says:

      Hah, no…I failed to let my quinoa cool before I mixed it in with the chocolate chips and, probably partly because I’d used mini chips (it’s all I had on-hand) they melted. It definitely looks like cocoa powder, but it’s just because my chips melted throughout the batter.

  3. Michelle says:

    These are yummy! They are kind of like oatmeal muffins in texture – nicely hearty. :-) Just a couple notes: my quinoa needed more water than that to cook until tender, and I ended up with extra – which is nice since I do use it in other dishes. I also made these with a gluten free all purpose mix (increased the b.p. to 2 teaspoons, and added 1 teaspoon of xanthan gum) and substituted non-dairy milk and they turned out very well. (Better than the non-g-free ones, but that was because I mis-measured the milk in the regular ones and so added flour and ended up with dense muffins that still tasted great.) :-)

    • kristi says:

      I usually end up with a bit of extra quinoa, too, but I had EXTRA water. Weird. Different types/brands of quinoa are probably all a little different. I love the sound of your g-free adaptations. Thanks for sharing!

  4. These muffins sound absolutely delicious, and so healthy too! What a treat!

  5. Jennifer says:

    I just made these muffins this morning. The only thing I did differently was use rice milk in place of the whole fat milk. I was a little worried about the big difference in fat so I added 1/4 cup flax meal. These muffins were great. They are mildly sweet, hearty, but not too dense. I will certainly make these again.

  6. Rachel says:

    Made these last night with just a few modifications to make them dairy free (unsweetened almond milk and frozen blackberries instead of the chocolate chips). And the kids DEVOURED them!!! Great recipe!!

  7. Christy says:

    I made these tonight for breakfast tomorrow. I didn’t think we were going to have any left for breakfast because everyone kept sampling them:-) They are great! Thanks for the recipe!

  8. Jessica says:

    No chocolate chips in the house– how would I use cocoa powder as a substitute?

    • Kelly says:

      You could probably add about 1/4-1/2 cup cocoa powder to the dry ingredients do give it a bit of chocolate flavor.

  9. shannon says:

    Yum! I’ve wanted some alternatives to using quinoa as a side dish for a long time but have never known what to do. These turned out great with white whole wheat. I thought the texture may be “weird with the quinoa but they are great.

  10. Kia says:

    I was wondering if you have tried to make these gluten free? Do you think all purpose gluten free flour might work as well?

  11. Nicole says:

    Ran out and bought a box of quinoa just for this! I’ve never had it before…. I melted my chocolate chips with the hot quinoa then added more chips so they are double chocolaty. I’ll never get the kids to eat them if it doesn’t scream chocolate! Thank you for the recipe!

  12. Courtney says:

    Just made this and I love them!!! They hit the spot!

  13. YES!! My daughter will love these, but I think I really need to substitute the chips for nuts instead!! This is one recipe I have to try!

    Thanks for sharing it!

  14. Kate says:

    I just made these. They were very nice!! Only problem I had was that the quinoa became crunchy on the bottom and I found myself not eating the bottom. If anyone has any tips on how to stop this from happening I’d be greatful. Also, next time I think I’d put in slightly less flour and quinoa and add another egg, as they were very dense, didn’t rise very much and I had lots of left over batter. Thanks very much for sharing. I think my little one is going to love them!

  15. Kelli says:

    Muffins are great. My whole family enjoyed. Next time I think I will add the quinoa while warm to melt the chips. Thanks for the recipe!

  16. marta says:

    I really want to make these, but I am a little confused how much quinoa to use. Do I use two cups of cooked quinoa in the recipe? Thank you.

  17. marta says:

    I’ve made these and they are so yummy. But, they don’t seem to last very long sitting on the counter. One time they started molding in two days and the next time, they got hard as rock in two days. Do you have any suggestions as to how to keep this from happening?

  18. Rebecca says:

    So yummy! I cut in half, spread little bit of peanut butter on and microwave for 20 seconds. SO GOOD!

  19. Ashley says:

    Does it have to be whole milk? We usually only keep skim on hand?

  20. Kristen says:

    I love this recipe. However mine came out very dense. I cooked them for 25 mins on 350 and used a almond milk instead of whole milk. Any suggestions to try next time?

  21. Kim says:

    Do you think these could be sweetened with bananas?

    • Lisa says:

      Kim – The recipe already calls for applesauce as a sweetener. Are you considering swapping the brown sugar? Or just adding banana for an additional sweetness kick?

  22. Lorraine says:

    Has anyone done mini muffins in paper liners? If so, how long did you bake? Thanks

  23. Kim says:

    Could this be made into a big cake?

    • Lisa says:

      Kim – I have never experimented with making this into a big cake. Sounds like it might work, if you do try it – let us know how it turns out!

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