Gluten-Free Lemon Poppy Seed Muffins

Lemon Poppy Seed Muffins from Queen of Quinoa (@alyssarimmer)I’ve been in love with lemon poppy seed everything ever since I saw this recipe for pancakes last year. It happened to be in my inbox on my birthday (happy birthday to me!) and it was all I could do to stop myself from leaping out of bed and making them right then and there. But my pantry wasn’t stocked and it was my birthday after all. It was the boy’s turn to make me breakfast, right?

And like many of my must-make recipes do, this got pushed to the back burner.

Lemon Poppy Seed Muffins from Queen of QuinoaIt wasn’t until recently, when I’ve started working on my newest book, that the fabulous lemon poppy seed combo popped into my head again. I wanted to make the pancakes, but my pancake chapter was getting pretty full, so I went the muffin route.

And muffins never tasted so good.

These gluten-free lemon poppy seed muffins are simply divine. A bright, yellow burst of sunshine in every bite.
Lemon Poppy Seed Muffins from Queen of QuinoaYou see, muffins have a special place in my heart. My sweet tooth (thanks, Dad) often gets the better of me for breakfast, whether that’s Saturday morning pancakes, Sunday morning waffles or a Monday morning muffin (well in this case Friday morning muffins). We’re a house of morning sweets and muffins are one of our favorite things to make.

As I’m working on my newest book (not sure if it will be an ebook or printed – what do you think!?), I’ve been making a ton of muffins. And this recipe for gluten-free lemon poppy seed muffins is my best recipe yet.
Lemon Poppy Seed Muffins from Queen of Quinoa (@alyssarimmer) Like all of my recent baked goods, these lemon filled beauties are not only gluten-free, but also dairy-free and refined sugar-free as well. But what is more spectacular is the texture. I’ve never in my life had a muffin as soft, moist, and cakey as these. It’s the kind of baked good that you’d never be able to say is gluten-free. They’re that perfect.

So wake up sunshine and get your bake on. These gluten-free lemon poppy seed muffins need to be on your breakfast table this morning.

And tell me, would you rather see a printed or digital version of my next quinoa cookbook?

Gluten-Free Lemon Poppy Seed Muffins

Prep Time: 10 minutes

Cook Time: 30 minutes

Total Time: 40 minutes

Yield: 12 muffins


  • ¾ cup sorghum flour
  • ½ cup toasted quinoa flour
  • ¼ cup millet flour
  • ½ cup tapioca starch
  • 1¾ teaspoon guar gum
  • 1½ teaspoon baking powder
  • ¼ teaspoon baking soda
  • ½ teaspoon fine sea salt
  • ½ teaspoon stevia powder (or more to taste)
  • ¼ cup light flavored oil (I prefer coconut oil)
  • ¼ cup unsweetened applesauce
  • ½ cup honey
  • Zest of two lemons
  • 2 large eggs
  • 3 tablespoons lemon juice
  • ¾ cup plain yogurt (I like Amande)
  • 2 – 3 tablespoons of poppy seeds


  1. Preheat the oven to 350 degrees F and grease a muffin tin with non-stick cooking spray.
  2. In a small mixing bowl, whisk together dry ingredients and set aside.
  3. In a medium mixing bowl, beat together oil, applesauce, honey and lemon zest until combined. Mix in eggs, one at a time, until creamy and smooth.
  4. Add ? of the dry ingredients into the wet ingredients and mix until just incorporated. Mix in lemon juice and ½ cup of the yogurt. Add another ? of the dry ingredients and mix again until just incorporated. Add the remaining yogurt and still until combined. Fold in the remainder of the flour, followed by the poppy seeds.
  5. Spoon the batter into the muffin tins, ¾ of the way full. Bake in the center of the oven for 30 – 35 minutes, until browned and a cake tester inserted into the center comes out clean.
  6. Cool in the pan for 5 minutes, then transfer to a wire rack and cool completely.


Baking with Quinoa by Alyssa Rimmer | Queen of Quinoa

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  • Rachel

    I have quinoa flour but its not toasted, can I just lightly toast it on the stove top?

    • Queen of Quinoa

      Hi Rachel – you sure can! Just throw it in a dry skillet and toast until it’s brown. Should only take a few minutes. I would suggest doing 1/4 cup at a time so it’s not over crowded. And make sure to let it cool completely before you add it to your baking. Hope you enjoy these muffins. They’re delicious!!

  • Susan

    What quantity for the poppy seeds? They are missing from the recipe/

  • Jennifer Darling

    Do you have the nutritional facts on these? I don’t see that anywhere. I’m mostly interested in the calorie and fat count.

    • Queen of Quinoa

      Hi Jennifer – I actually don’t have nutritional info on my site. I strive to make clean, healthy food that is as nutritious as possible. My thought is all in moderation, so have one, and you’ll be okay. At least that’s my philosophy. I’ve hear that Sparkrecies is a place you can enter ingredients and find nutritional info. Check it out!

      • Jennifer Darling

        Thank you so much for the reply. I agree, but when I’m in calorie counting mode (like now), it helps. That website sounds interesting. I’ll definitely check it out. Thank you!

  • siewlingchaw

    is it a must to add the tapioca starch into the recipe if i choose to use normal whole wheat flour instead since i’m not so into gluten free diet?

    • Queen of Quinoa

      Absolutely not :) If you’re using whole wheat flour or just regular old AP flour, you won’t have to add any of the gluten-free ingredients. Just beware your liquid ratio might be a tad different. Keep an eye on the texture and add any additional liquid if it seems to dry. Enjoy!

  • Betty

    Can I add almond milk instead of yogurt? since I have to be dairy free.

    • Queen of Quinoa

      I used almond milk yogurt actually. You could also use coconut milk yogurt. I don’t suggest using almond milk because it has a much higher water content and would change the texture of the muffins. If you haven’t ever tried almond yogurt, I recommend that brand Amande. It’s spectacular!