Chocolate Chip Pumpkin Quinoa Muffins

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Chocolate Chip Pumpkin Quinoa Muffins

The Cook
12 Servings
13 Ingredients

Tis the season for pumpkin! And in our house – the best compliment to pumpkin is chocolate of course! These chocolate chip pumpkin quinoa muffins make an excellent fall breakfast or afternoon snack!

12 Servings
13 Ingredients


  • ¾ cups Brown Sugar
  • 1 ¼ cups Flour, Whole Wheat
  • 1 ½ teaspoons Pumpkin Pie Spice
  • 1 teaspoon Baking Powder
  • ½ teaspoons Salt
  • ½ teaspoons Baking Soda
  • ¾ cups rinse, drain, and cook Quinoa
  • 2 individual Egg
  • ¾ cups Pumpkin, Canned
  • ½ cups Milk
  • ¼ cups melt Butter
  • 2 teaspoons Vanilla Extract
  • ½ cups Chocolate Chips, Mini



  • 12.Muffin Liners
  • Labels
  • Muffin Tins

Cooking Instructions

Freeze For Later Cooking Day Directions


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Make From Frozen Serving Day Directions

Easy Assembly/Ready to Eat

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Make It Now Cooking Directions

Oven Cook

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Nutrition Facts

  • Not available.


Join the discussion
  1. You could not have posted these at a better time! I bought all these ingredients with the plans to make pumpkin chocolate chip muffins for a road trip and I always have quinoa on hand. Thank You!!!

  2. Is that 3/4 cup of quinoa cooked and drained the before or after cooking measurement? (Never cooked it before so I am not sure if the before and after cooking measurements are different like rice and pasta, or not!) I have a trial size package that is 1/2 cup uncooked and I am trying to decide if I can use that, or if I need to go to the store!

    1. You shouldn’t have to ‘drain’ the quinoa once it is cooked. If you do, then either the quinoa isn’t done, or you used too much water, which in the latter case, you will end up with a very mushy product 🙁 . I never use the amt of water recommended…for 2c of dried quinoa, I use about 2 3/4c water. Comes out crunchy and great! Don’t forget to rinse it to get all the bitterness out! 🙂 Good luck!

    1. Anna – I am sure you could make it into a loaf. Just cook until a knife inserted in the center comes clean. I would apx an hour. Let us know how it goes

  3. Have you ever tried using quinoa flour with this, or any recipe for that matter? I see it all the time in the store but have not tried it myself! Wondering if you can just substitute it in for regular flour…

  4. Unlike most of America, I’m not a big fan of pumpkin in my baked goods. Do these taste like pumpkin or is it mainly for keeping them moist? Can I substitute something else??

    1. Yes – there is a flavor of pumpkin to these delicious muffins. You could substitute a butternut squash or apple puree if Pumpkin isn’t your thing.

  5. I have never seen “pumpkin pie spice”. What exactly is it? Can I use some different spices? Can’t wait to try this recipe! 🙂

    1. Britt-
      Pumpkin Pie spice will be with all of your other spice blends. Basically it is a mix of cinnamon, nutmeg, cloves and ginger. And you can certainly make your own using those spices! Good luck!

    1. I haven’t tried with GF Flour – but I would think if you have a flour that works well in baking, that it would work with this recipe!

  6. Think they would work okay with regular ol’ white flour? I know the whole wheat is healthy, but I don’t have any on hand and I’m too lazy to go to the store… I really want to make these!

    1. Made double batch 2 days ago using white flour ( ididn’t realize until I read your post that I should have used whole whea LOL) and they turned out great, family devoured them in day ans a half and have requested me to bake more today!

  7. I think the “complete protein” thing has been dis-proven or de-emphasized or something. You can “combine” meals over 2 days so no need to eat all your amino acids together. But still they sound great!

  8. I made these a couple days ago and my kids and I are all loving them! Yummy! Couple questions though. How can I make this recipe dairy free? My quinoa turned out a little crunchy in the muffin. Should I cook it less before adding it to the mix?

    1. Lacie-
      My quinoa was a little crunchy as well – but we seemed to like it! But if you do not like it that way – yes I would cook it a little longer.

  9. Hi,
    These are great muffins! I wanted to share that I substituted in .25 cup almond flour in with the whole wheat flour (reduced to 1 cup) and it turned out great. My quinoa wasn’t crunchy and I found the muffins very moist too. I plan on making these muffins a lot

  10. I made these, just did 1/2 a batch & Loved them. My substitutions were Cocount Oil in place of butter & chopped fresh cranberries in place of chocolate chips. I used a Trader Joes TriColor Quinoa.
    Definitely pinning to make again. I may try Honey in place of sugar too. Thanks for Yummy recipe!

  11. Made these today and they are awesome. We used freshly ground whole wheat pastry flour in them. I made them into muffin tops because they are easier for my youngest to eat without making a mess. Both of my boys love them and I love that they sneak some extra protein in for my picky eater!

  12. Yummm!…have made 4 times now. I make vegan by replacing the eggs with 2 Tbsp ground Flax + 6 Tbsp water (do this first and let it sit x 5 minutes), dairy free milk, and Earth Balance or coconut oil in place of butter. For sweetness: instead of the brown sugar use 1/4 cup sugar and 2 Tbs molasses. And I use 1 cup of cooked quinoa.

    1. I plan on veganizing these too. Did you use the Enjoy Life chocolate chips?
      I usually use 1 tsp of flax and 2 tbsp of water per egg called for. I’ve heard of people using apple sauce or banana in place of eggs too. I’d be curious if the banana worked, as it might match the pumpkin and choc chip.
      I would think the molasses would be heavy, wouldn’t it? I plan to use turbinado, or brown rice syrup, or maple (yum).
      I’ll be using soy milk, as that’s all my son will drink, but think coconut milk would work lovely!
      Please let me know if you’ve tried any other vegan options in this recipe, what has worked and what hasn’t. Thanks!

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