Grab a glass of green juice, freshly brewed coffee, and start your mornings with these herb quinoa muffins. Made with the king of grains, protein-rich quinoa, these muffins provide a hefty dose of muscle-building amino acids. They’re rich in omega 3 fatty acids, slow-burning carbohydrates, vitamins and minerals – nothing like their nutrient-deprived counterparts. Constructed from hand picked, natural ingredients, savory flavors are used to create a new spin on the morning classic.

We pulled this perfect A.M. recipe from chef Amy Chaplin’s latest cookbook, At Home in the Whole Foods Kitchen, this plant-based creation is only one of many soul-nourishing recipes that lie between the pages of this book. It contains vegan and naturally gluten-free staple recipes — from simple every day meals to special occasion dishes. And the book’s recipes are organized into two parts. Part one explores the pantry, with everything you need to know to stock your kitchen with nutrient rich ingredients. Part two celebrates each season with recipes that show off local produce at its peak, such as chia pudding and butternut squash lasagna. Here’s Amy with a few notes on how she created our new favorite breakfast recipe…

The first time I tested this muffin recipe and ate one warm from the oven, I couldn’t believe how much I enjoyed it. The mashed sweet potato in the batter adds a pleasantly moist and sweet background to the onions, herbs, and delicate crunch of black quinoa. For a variation, try substituting winter squash for the sweet potato and adding rosemary in place of thyme. You can also use ½ cup of any leftover cooked grain in place of the black quinoa. Toasted pecans or walnuts are a tasty addition to the mix too. Whatever you use, your kitchen will smell inviting, and you’ll end up with a delectable savory treat.

Herbed Black Quinoa Muffins
makes 10 muffins


For the quinoa:
¼ cup black quinoa, washed and soaked 12 to 24 hours in 1 cup filtered water
¼ cup filtered water
pinch sea salt

For the muffins:
2 Tbsp ground flax seeds
¼ cup plain soy milk or plain nut milk
¼ cup plus 1 Tbsp extra virgin olive oil, divided
1 medium onion, diced
2 Tbsp chopped sage leaves
2 tsp chopped thyme, plus thyme sprigs to garnish
1 tsp sea salt, divided
1½ cups sprouted spelt flour or sprouted whole-wheat flour
1 Tbsp aluminum-free baking powder
¼ tsp baking soda
1 cup mashed sweet potato (see notes below)
¾ cup filtered water
2 tsp unpasteurized apple cider vinegar
1 tsp tamari


For the quinoa:
Drain and rinse quinoa. Place in a small pot, add water, and bring to a boil over high heat. Reduce heat to low, cover pot, and simmer for 15 minutes or until all water is absorbed. Remove from heat and allow to sit, covered, for 10 minutes; fluff with a fork. Measure out ½ cup and set aside. Save the remaining couple of tablespoons of quinoa to sprinkle over muffins.

For the muffins:
Preheat oven to 350 F. Line a regular muffin pan with 10 paper liners.

Place flax and soy milk in a medium bowl and whisk to combine. Set aside to thicken while you cook the onion.

Warm 1 tablespoon olive oil in a skillet over medium heat. Add onion and sauté for 5 minutes or until golden brown. Add sage, thyme, and ½ teaspoon salt; reduce heat to low and continue cooking for another 5 minutes or until caramelized. Remove from heat and set aside.

Sift flour, baking powder and baking soda into another medium bowl. Whisk to combine and set aside.

Add sweet potato, water, vinegar, tamari, and remaining ½ teaspoon salt to the flax-soy milk mixture and whisk until smooth. Add remaining ¼ cup olive oil; whisk again and add flour mixture. Use a rubber spatula to stir mixture gently until almost combined, then fold in cooked quinoa and onions.

Divide batter between lined muffin cups, filling them all the way to the top. Garnish each muffin with a thyme sprig and a sprinkle of remaining cooked quinoa. Bake 45 to 50 minutes or until a toothpick inserted in the center comes out clean. Remove from oven; leave muffins in the pan for 5 minutes before transferring them to a wire rack to cool slightly before serving. Once cool, any leftover muffins can be stored in an airtight container in the fridge for up to two days.

Notes: For 1 cup mashed sweet potato, peel 1 medium sweet potato (14 oz) and cut it into rough ½-inch dice (about 2 cups). Place in a steamer basket over boiling water, and steam for 5 minutes or until soft. Remove from heat, transfer to a bowl, mash with a fork, and measure out 1 cup.

If you forget to soak the quinoa, increase the water by 2 tablespoons and cook for 20 minutes.


From ‘At Home in the Whole Food Kitchen’ by Amy Chaplin, © 2014 by Amy Chaplin. Photographs © 2014 by Johnny Miller. Reprinted by arrangement with Roost Books, an imprint of Shambhala Publications Inc., Boston, MA. 

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  1. I must have done something wrong because the batch I made was still raw on the inside after 55 min of baking at 350 degrees. The tops were perfectly done so I cut them off so we had something to eat with our soup and put the remainder back in the oven. After another 15 minutes, still not cooked through : ( I reviewed the recipe but don’t see anything that I missed. Any thoughts?

    Linda B. | 01.26.2015 | Reply
  2. Make them even smaller next time. So make a larger amount of smaller muffins to ensure they’re cooked all the way through.

    Tasha | 03.11.2015 | Reply
  3. This looks so yummy, what a cool recipe. Its always really hard to find a good vegan muffin recipe 🙂

    Renee | 09.24.2015 | Reply
  4. Just made these and had the same issue. raw in the middle. will make mini muffins next time as the flavour was good.

    Stef | 03.30.2016 | Reply
  5. Mine were raw too. I cooked half a large batch and half mini muffins and the mini ones were raw too. Even put them back in for an extra ten minutes and they just dried out on the outside and raw in the middle. Wondering if the quantities are off?

    Chelsea | 08.01.2016 | Reply
  6. Thanks for finally writing about >A Vegan Morning: Herb Quinoa Muffins from Amy Chaplin <Loved it!

    all natural soap diy | 01.17.2018 | Reply
  7. I am excited to see yr method of cooking soaked quinoa. I’ll make these muffins as soon as possible & report back. Thank you

    Laura | 05.07.2018 | Reply
  8. Totally raw in the middle. I’m really disappointed by this recipe as a lot of work went into these—making the quinoa, caramelizing onions, cooking sweet potatoes. There needs to be a way to test for fineness as the toothpick method did not work. I tried to get my chickens to eat these and they weren’t having it.

    Brooke | 08.26.2019 | Reply
  9. Sorry *doneness not fineness

    Brooke | 08.26.2019 | Reply
  10. Phew! Glad I read the comments about being raw in the middle before trying to figure out what gluten-free flour to use as a substitute as these NOT gluten free (not even using spelt) so please do not make that claim.

    Shans | 11.26.2019 | Reply
  11. I baked them for 50 mins, and they are cooked perfectly! Toothpick came out clean when i tested for rawness. When I opened one up while it was hot, it appeared like it might be raw but as it cooled down it finished cooking through and was moist & perfectly done.
    I didn’t have sweet potato, so I subbed canned pumpkin, which worked great. Next time I’d love to try with sweet potato, or at least a little drizzle of maple syrup if I do pumpkin again. I think it was missing a little touch of sweet with the savory, but that’s my fault!
    I also used red quinoa instead of black with no problem.
    Nice healthy breakfast muffin! Thank you!

    Crystal | 07.07.2022 | Reply

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