Gluten Free Lemon Poppyseed Muffins

September 4, 2020
At a Glance


Baking these lemon poppyseed muffins with sour cream and a full lemon’s worth of juice and zest makes for the most tender crumb in muffins that are bursting with flavor and crunch.

Prep / Cook Time

10 minutes / 20 minutes


 5/5 (9 votes)
Gluten Free Lemon Poppyseed Muffins

These gluten free lemon poppyseed muffins have all the brightness of lemon and the nutty crunch of poppyseeds in a tender sour cream muffin.

Lemon Poppyseed muffin cut in half on small white plate

The pleasure of baking with lemons

Bite into these lightly sweet muffins through a thin layer of sugar crunch, and they’re super soft & moist inside. The poppyseeds add a pleasant fruity crunch.

Lemons are like the salt of the citrus world. They make everything better. Even just a bit of lemon squeezed over your dinner or into your favorite cake will brighten everything up.

Closeup image of lemon poppyseed muffin on small white plate

Growing lemons

I don’t have a lemon tree in my yard or anything. But I would very much like to move somewhere I could have a lemon tree in the yard. 🍋

Sometimes I see people growing lemons indoors. I live in N.Y., but I wonder if I could grow them in a container, and bring the tree indoors during the cold months.

I imagine myself lovingly pruning my tiny lemon tree, and think my dream might come true. But then I remember. I have 2 cats and 3 dogs and the dream dies.

Raw lemon poppyseed muffin batter in muffin tin wells

Can you substitute chia seeds for poppyseeds?

If you just don’t happen to have poppyseeds on hand, consider buying them. They’re so good sprinkled on all kinds of things, from bagels to salads.

But if you can’t have poppyseeds, or you’re afraid of failing a drug test after you eat poppyseeds because they may contain very small, trace amounts of opium extract, you can replace them with chia seeds.

Black chia seeds look a lot like poppyseeds, but they’re larger and denser when they’re dry. That will make them more distracting than poppyseeds when you bite into the muffin.

Instead of mixing the chia seeds into the dry ingredients that get whisked together, try adding them to the wet ingredients. It might help them soften up a bit before baking.

This isn’t our only lemon poppyseed recipe. Case in point, our lemon poppyseed cookies. So please share your results, and let’s learn together. 

Lemon Poppyseed muffins overhead image with one cut in half

Ingredients and substitutions


If you can’t have butter, you can try replacing it with Melt or Miyoko’s Kitchen brand vegan butter. They’re my favorite butter substitutes.

You might also be able to use Earth Balance buttery sticks in this recipe in place of butter, but you might find that your muffins rise more and then fall more. Earth Balance has more moisture than butter, so the balance of ingredients will be disturbed.

If you can’t have sour cream, plain Greek yogurt is a great substitute. If you can’t have dairy yogurt and can’t find nondairy plain Greek yogurt, try straining plain nondairy yogurt until it’s the proper consistency.


There are three whole eggs in this recipe, and they’re really important to the rise and texture. I don’t recommend trying to replace each of them with an egg replacer, but if you’d like to try, go with one “chia egg” per egg (1 tablespoon ground white chia seeds + 1 tablespoon lukewarm water, mixed and allowed to gel).

Lemon Poppyseed Muffins in an array overhead, and one single half muffin on a white plate

Like this recipe?

Prep time: Cook time: Yield: 12 muffins


2 cups (280 g) all purpose gluten free flour (I used Better Batter; you must use one of my recommended blends)

1 teaspoon xanthan gum (omit if your blend already contains it)

1 teaspoon baking powder

1/2 teaspoon baking soda

1/2 teaspoon kosher salt

3/4 cup (150 g) granulated sugar, plus more for sprinkling

Zest and juice of 1 lemon, separated

2 tablespoons poppy seeds

8 tablespoons (112 g) unsalted butter, at room temperature

1 cup (240 g) sour cream, at room temperature

3 eggs (150 g, weighed out of shell) at room temperature, beaten


  • Grease or line a standard 12-cup muffin tin and set it aside. Preheat your oven to 350°F.

  • In a large bowl, place the flour, xanthan gum, baking powder, baking soda, salt, 3/4 cup granulated sugar, lemon zest, and poppy seeds, and whisk to combine well. In a separate, 4 cup measuring cup or bowl, place the butter, sour cream, lemon juice, and eggs, and whisk until very well combined and smooth. Create a well in the center of the dry ingredients, and pour in the wet ingredients. Mix until just combined.

  • Fill the prepared cups of the muffin tin full. Smooth the tops of the batter with wet fingers. I recommend you sprinkle the tops with a light sprinkling of additional granulated sugar (about 1 1/2 tablespoons total for all the muffins)—but that step is optional. Place the muffin tin in the center of the preheated oven, and bake for about 20 minutes, or until a toothpick inserted into the center of a muffin comes out clean. Allow the muffins to cool in the muffin tin for about 5 minutes before transferring them to a wire rack to cool before serving. Completely cooled leftovers can be sealed tightly, then frozen. Defrost at room temperature or in a microwave oven.

  • Originally published on the blog in 2012. Photos, video, and text new; recipe modified slightly.


  • Sophie
    September 19, 2020 at 3:18 AM

    Love this recipe! I did try chia seeds once in a lemon poppyseed bread and it definitely messed up the texture. I’m thinking I could have skipped one of the eggs perhaps. Not really my thing, I prefer the poppyseeds they’re just hard to come by where I live. I haven’t tried chia seeds in this particular recipe though!

  • Dana Vanderhedyen
    September 11, 2020 at 8:34 PM

    I can only get Robin Hood gluten free flour – will this work?

    • Nicole Hunn
      September 12, 2020 at 8:05 AM

      I’m afraid I don’t recommend that, no, Dana.

    September 4, 2020 at 7:32 PM

    I’m going to mix some lemon zest with the sugar for topping the muffins also. Love the tartness.
    Also yes you can grow a miniature lemon tree in a large pot. Put a small decorative fencing around the inside of the pot to deter the cats and dogs from sniffing. When you bring it inside make sure it still gets lots of sun.

    • Nicole Hunn
      September 5, 2020 at 7:32 AM

      Great idea, Carol. Thank you for the suggestion about the lemon tree! I’m just imagining my cats jumping on it and knocking it over, and the dogs just, like, eating the dirt at the very least.

  • Emily
    September 4, 2020 at 11:27 AM

    Can you specify what adaptations I would need to make this into a loaf instead of cupcakes? Liquid changes, or baking time? Thanks!

    • Nicole Hunn
      September 4, 2020 at 12:41 PM

      This recipe is not suited to making a loaf instead of muffins, Emily. I do have a recipe for lemon poppyseed quick bread. It’s always worth doing a quick search on the blog!

  • Patti
    April 30, 2012 at 9:48 AM

    Made these this week-end. I did dip the tops in a melted butter/lemon combo & then a touch of sugar after baking. To die for! If my gluten eating family rants & raves, it is in my cooking repertoire & they did.

    Thanks Nicole!

  • Judy
    April 29, 2012 at 10:21 PM

    Yum, oh yum, oh yum! Everyone loves these! I plan to take some for my friend’s husband who must eat GF when I visit this week. (I subbed Splenda for the sugar since I’m trying to cut carbs. Exceptional. Thank you!

  • RebeccaLB
    April 24, 2012 at 12:53 PM

    Yum, yum, yum! My favorite muffins! My dear strong-silent-type husband can’t tolerate seeds so for him I add freeze dried strawberries! He calls them Strawberry-Lemonade muffins.

  • Nicole
    August 4, 2011 at 8:58 PM

    Hi, Annette,
    Good to know that the recipe works well with blueberries! Oddly, I have never played with this recipe, so I’m glad to know that you were able to do that with success. Thanks for letting me know. :)
    xoxo Nicole

  • Sarah
    April 30, 2011 at 11:41 AM

    Haha, very cute.

    Lemon is my favorite flavor and I do love muffins. Can’t wait to make these!

  • April 24, 2011 at 6:34 PM

    I made these today using the potato starch sub you suggested. They are still a bit moist inside but DELICIOUS!! A definite winner recipe that will be a regular around here! Thanks!!

  • Amy
    April 21, 2011 at 8:25 PM


    Another awesome recipe! We loved the muffins . . .and my husband isn’t crazy about anything lemony and he LOVED them! Thanks for continuing to make us gluten free eaters so happy!!


  • April 17, 2011 at 4:33 PM

    These are in the oven right now, can’t wait to taste them they smell so lemony and yummy!! Thanks for all your help Nicole. My husband is similar, doesn’t say much, eats what I make. Every once in awhile he’ll compliment something so then I know it must be good!

  • April 17, 2011 at 2:14 AM

    What luck! It turns out I have all of these ingredients on hand, even the poppy-seeds (as I recently made your Everything Bagels), and I had been meaning to attempt lemon poppyseed muffins someday. Someday shall be Sunday.

    Regarding secrets… I grew up eating fairly healthy food that was high in vegetables and low in meat. Processed food was relatively rare in our house. One day, I confessed to my mom that I secretly liked sandwiches at other people’s houses that made with Wonder Bread, lunch meat, processed cheese and mayo. She laughed and said, “Actually, I secretly like them, too.”

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