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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

4.54 from 139 ratings
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!
Prep Time: 15 minutes
Cook Time: 15 minutes
Total Time: 30 minutes
Servings: 12 muffins
Print Rate Pin


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:

  • Preheat oven to 400 degrees and line a 12-cup muffin tin with paper liners or spray with non-stick spray.
  • 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.
  • In a medium bowl, whisk together the eggs, fresh lemon juice, lemon extract, oil, and coconut milk until completely combined.
  • 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.
  • 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:

  • 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.

Nutrition Information

Serving: 1g | Calories: 187kcal | Carbohydrates: 31g | Protein: 2g | Fat: 7g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 4g | Sodium: 175mg | Potassium: 6mg | Fiber: 2g | Sugar: 17g | Vitamin C: 0.01mg | Calcium: 73mg | Iron: 1mg


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Nutrition Facts are estimated and aren't always accurate. Please consult a doctor or nutritionist if you have special dietary needs.

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4.54 from 139 votes (134 ratings without comment)

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Recipe Rating

  1. Keren says:

    Wow!!! I made them today and they came out absolutely delicious! Probably one of the best muffins I’ve ever made. Can’t wait to try more of your recipes ❤️

  2. Rhea says:

    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!

  3. Jill Grimes says:

    These taste AMAZING!! I’ve been GF for 11 years now, and these are the best lemon poppy seed muffins I’ve ever had- pre AND post-GF. Congrats! Ordered your cookbook & tweeted this recipe. As a family physician, I get many requests for GF recipes/cookbooks. Happy to add yours to my list. KUDOS!

  4. Julie says:

    This recipe was amazing! Thank you so much! I am GF, dairy free and tree nut free, so finding good recipes can be challenging. I used soy milk in place of dairy/coconut milk and it worked great! My kids also loved them, they are 8 and 10, so great option for kids! I found myself licking the glaze bowl, that stuff was so amazing!! Thank you again!

  5. Chrissy says:

    5 stars
    These are so easy and so delicious! My husband doesn’t eat GF and loved them as well, I had to hide them… And wished I made a double batch!

  6. Elizabeth Fisher says:

    Absolutely delicious!

  7. Susan Diehl says:

    5 stars
    I made these for my GF, egg free, dairy free son. The verdict: “I liked it.” lol They turned out light and pretty with a nice crumb. I used coconut milk and Just Egg plant-based egg replacement.

  8. Susan Diehl says:

    I made these with Just Egg plant-based egg replacer and they turned out well.

  9. Susan Diehl says:

    I made these today during the Covid 19 lockdown so that my gluten free, milk free, egg free son could have some comfort food. I used coconut milk and Just Egg liquid plant-based egg replacement (made of mung beans). I didn’t have lemon extract, so I used 1/8 t lemon oil. I used Bob’s Red Mill GF All Purpose Flour. They domed very nicely in the oven and did sink a bit once I took them out, retaining a less pronounce dome (still not flat though). Crumb is nice and muffins are light at first bite, but do become a bit gluey as you chew (could be the egg replacement). If I make these again, I think I will make them a bit sweeter and try it with the lemon extract. Overall I was excited that these turned out as “normal” as they did with so many substitutes!

  10. Amanda says:

    If the flour mix used already has anthem gum, do we still add more of it?

  11. Justina says:

    These were amazing! Thank you so much for sharing the recipe. I made mine dairy free, but also egg free by whipping 1/2 cup of aquafaba with 1/2 teaspoon of cream of tartar to stiff peaks and folding it into the batter at the end. They came out light and fluffy and delicious!

  12. Tracy says:

    These are awesome! I made them dairy free and also use a sugar sub. Monk fruit sweetener is the best! No weird after taste at all! I will be keeping this recipe in my own recipe box! Thank you for this one!!

  13. Michelle Duncan says:

    Hi! Thanks for your recipe! I made these today and they turned out perfect! I used 1 cup of bobs red milk 1:1 flour, 1/2 cup almond flour and 1/2 cup oatmeal flour! I also like to soak my poppyseeds in the milk for a few minutes to let them soften up! I will be saving this recipe for the future!

  14. Dianne says:

    5 stars
    Can I substitute a different oil for the avocado?

  15. Dianne says:

    5 stars
    Can I substitute a different oil for the avocado?

  16. Jean says:

    4 stars
    How do you think the sugar replacer Stevia would work in this recipe?

    • Sharon says:

      I haven’t tried this with a sugar sub, sorry!

      • Jeri Greenwold says:

        For substitutes, I used coconut sugar as well as part almond milk and coconut water since I didn’t have coconut milk and don’t use regular milk. They were darker because of the sugar, but still tasted great!