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Gluten Free Lemon Poppy Seed Muffins

Gluten Free Lemon Poppy Seed Muffins are really simple to make and are loaded with bright lemon flavor. These muffins can easily be made dairy free too!

gluten free lemon poppy seed muffins on a brown wood platter

Gluten Free Lemon Poppy Seed Muffins

There was recently an article in Food Network magazine that debated the difference between muffins and cupcakes. There really isn’t too much of a difference other than the fact that cupcakes are embellished with frosting and decorated with chocolate, sprinkles, or anything pretty.

Muffins are basically the less fancy version. Muffins are staying in to watch movies with friends while cupcakes are going to the gala.

But the batter is pretty much the same (other then the poppy seeds). Though for the sake of breakfast appropriate, I usually add a little less sugar to muffins than I do with cupcakes.

To get down to it though, I’ve been testing a lemon poppy seed muffin recipe on and off for the last year. I just haven’t been entirely happy with the results I’ve been getting. I’m a big fan of bakery style muffins – you know, the ones that really are like cupcakes but without the frosting.

Using a spoon to put lemon glaze on a gluten free lemon poppy seed muffin

They’re so moist and “light” but almost dense at the same time – like cake. But they’re so laden with oil/fat that it’s hard to justify making them like that unless it’s a special occasion. I wanted muffins that are good for every day eats. Ya feel me?

But after experimenting with muffin after muffin, I decided I wanted to try a version of gluten free lemon poppy seed muffins based off of my gluten free lemon cupcakes recipe. I mean, after Food Network even said that they’re similar, I decided to just go for it.

You guys, I should have done this earlier. This was really close to the muffin I’ve been searching for! The flavor was similar to a bakery style muffin. They just needed a liiiitle bit of tweaking so it wouldn’t break the calorie/fat bank at breakfast. Always with the recipe tweaking… 🙄

So for the cupcake/muffin version, I did end up adding a little more flour to help them dome and I reduced the liquid a bit because if the batter is too wet, it could prevent it from rising. After all the experimenting I had to do, I found that I actually do like my muffins to be a little “drier” then a cupcake.

Half of a gluten free lemon poppy seed muffin on a wood platter of muffins.

Domed Tops VS. Flat Tops

The cupcake version comes out nice and flat, the way a cupcake should be. But for the muffins, I wanted a bit of a domed top. I asked in an Instagram stories poll a while back and you guys all said domed muffins were a must.

So, how do we get that sought-after domed muffin top? Baking at a higher temperature. Baking at 350 degrees will give you a flat top, baking at 400 degrees will give you a dome. Nice and simple!

However, with that being said, I do find that any gluten free baked goods baked with fresh lemon juice just don’t rice as well. I find that with gluten free lemon bread too.

close up of gluten free lemon poppy seed muffin with a slice of lemon for garnish

The Great Debate

I also tried making a version of this muffin from my gluten free lemon poppyseed bread recipe – I didn’t love that version as much; which was surprising because I really like that bread. That recipe is also strikingly similar to the gluten free lemon cupcakes which leads me to another question – what’s the difference between quick bread and cake baked in a loaf pan 🤔

I guess that must also come down to frosting (though some breads are glazed) and the time of day you’re eating it?

But back to the muffin vs. cupcake debate – I guess I’m proving Food Network wrong then, there should be a difference between cupcakes and a muffin other than the topping. If it came down to a blind taste test, I would want them to be distinguished between breakfast and dessert.

Mission accomplished. And now I’m off to restock my fridge and pantry because I seriously baked about 10 batches of these gluten free lemon poppy seed muffins to get them right …

Whatever. It tastes good so lets just eat it, ok? Enjoy!

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gluten free lemon poppy seed muffins on a brown wood platter

Gluten Free Lemon Poppy Seed Muffins

Yield: 12 muffins
Prep Time: 15 minutes
Cook Time: 15 minutes
Total Time: 30 minutes

Gluten Free Lemon Poppy Seed Muffins are really simple to make and are loaded with bright lemon flavor. These muffins can easily be made dairy free too!


For the Muffins:

  • 2 cups gluten free all-purpose flour (see notes)
  • 1/4 teaspoon xanthan gum
  • 1 Tablespoon poppy seeds
  • 2 teaspoons aluminum free baking powder
  • 1/4 teaspoon baking soda
  • 1/2 teaspoon fine sea salt
  • 2/3 cup granulated sugar
  • zest from 1 medium lemon
  • 2 large eggs, room temperature
  • juice from 1 medium lemon
  • 2 teaspoons lemon extract
  • 1/3 cup avocado oil
  • 1/2 cup milk or unsweetened coconut milk (see notes)
  • 1/2 cup powdered sugar
  • 2 teaspoons fresh lemon juice (about 1/2 a medium lemon)
  • zest from 1 medium lemon


To Make the Muffins:

  1. Preheat oven to 400 degrees and line a 12-cup muffin tin with paper liners or spray with non-stick spray.
  2. In a large bowl, whisk together the gluten free flour, xanthan gum, poppy seeds, baking powder, baking soda, salt, granulated sugar, and lemon zest. Set aside.
  3. In a medium bowl, whisk together the eggs, fresh lemon juice, lemon extract, oil, and coconut milk until completely combined.
  4. Pour the wet ingredients into the dry ingredients and mix until just combined. Transfer the batter to the 12 muffin cups, they will be almost filled.
  5. Bake at 400 degrees for 14-15 minutes or until done. Do not over-bake. When done, remove from the baking pan immediately and cool completely on a wire rack. Cool before adding the glaze.

To make the glaze:

  1. Add the powdered sugar, fresh lemon juice, and lemon zest to a small bowl. Stir together until smooth. Drizzle over cooled muffins or use a spoon to cover the tops like a glaze.


  • I use my nightshade-free gluten free flour blend in this recipe with great results.
  • These muffins are best the day of. Freeze muffins if not using right away and defrost at room temperature.
  • Use up to 3/4 cups of milk in this recipe if you prefer a moister muffin.

Did you make this recipe?

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Friday 24th of March 2023

disregard - I see it now!!


Friday 24th of March 2023

Silly question but step 4 does not say to add the oil... but I'm assuming we would or is it a substitution for something else?


Thursday 21st of April 2022

Easy and quick to whip up. I was really looking forward to these because of all of the reviews and comments; however, I was disappointed. These taste strongly of lemon extract. I would have preferred more “real lemon” flavor and maybe a bit more tartness. I should have compared the recipe to other lemon poppyseed recipes to notice the extract. That said, spot on for texture! My family didn’t notice that these were GF.


Friday 21st of May 2021

I am horrible at baking and can't believe how well these turned out! I used dried lemon peel, and store bought lemon juice, still good! I'm amazed!


Thursday 27th of May 2021

Thanks Rhea!

Katie Brownlee

Sunday 25th of April 2021

I made these with King Arthur GF 1 for 1 flour. They were dense and delicious. My husband said, "Are you sure they are GF?" I did add some vanilla extract and lemon extract. Otherwise no changes. Since they aren't overly sweet, I'm going to try to add a lemon glaze. Thanks for the recipe!

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