Lemon flavor is the hero in this decadent gluten free lemon poppy seed muffin recipe. Top them with a lemonade icing drizzle, or enjoy them plain. They make a delicious addition to breakfast or brunch. These muffins are also dairy-free!

A lemon poppy seed muffin on a plate.

My kids were pretty excited about this new recipe because I love making fluffy muffins. Whenever I bake something with lemons, I send them out to pick a lemon or two from our tree. We are lucky to have fresh lemons most of the year.

I make a lot of muffins, and I share many of them here on Fearless Dining. All of my muffin recipes are freezable, so you can enjoy them anytime. Here are some of our favorite gluten free muffin recipes, or you can try this delicious gluten free strawberry muffins recipe!

Why these gluten free lemon poppy muffins are so good:

  1. These are the fluffiest gluten free muffins. They are seriously good!
  2. They are gluten- and dairy-free, making them great for those who must avoid both in their baking.
  3. My moist lemon poppy seed muffins are freezable, so you can make a double batch and freeze the extras. This allows you to have a ready-made grab-and-go breakfast!
  4. This is an easy recipe, and I share all of my tips and tricks so you can make them regular or with a big dome top!
  5. This recipe uses simple ingredients that you can find at any local grocery store. These fluffy muffins taste like the real deal and get rave reviews! Nobody will know these homemade muffins are gluten free.

Hands down THE best lemon poppyseed muffin I have EVER HAD!! Made these this afternoon and they are INCREDIBLE!! Moist and fluffy and they’re actually amazing on their own without
the icing. This one is a keeper!”

Chelsey T., Pinterest user

Allergen Information:

These homemade lemon poppy seed muffins are gluten-free, dairy-free, soy-free, oat-free, and nut-free.

All of the ingredients to make these lemon poppy seed muffins.

Ingredient Notes:

For the full list of ingredients and amounts, please go to the recipe card below.

  • Gluten Free Flour Blend – I tested two gluten free flour blends: King Arthur Measure for Measure and Bob’s Red Mill 1:1 GF Blend. One reader wrote and told me Namaste flour blend also works.
  • Poppy Seeds – These add the perfect texture to this muffin recipe.
  • Non-Dairy Milk – I used almond milk, but other plant-based milk or regular milk are also fine. I would avoid using canned coconut milk. It is too dense of a liquid for this recipe.
  • Eggs – I recommend size large eggs.
  • Coconut Oil – Regular or vegan butter also works well if you prefer to use one of these instead of oil.
  • Lemon – You can use fresh lemon juice or bottled.

Expert tips for the fluffiest muffins:

  • Muffin tip: If you over-mix the batter, your muffins will not be as light and fluffy! Mix the wet and dry ingredients until they are just barely mixed!
  • Do NOT use a standing or an electric mixer for best results. They will overmix the batter.
  • If you want your muffins to have a domed style top, bake at 425º F for the first 5 minutes, then reduce the temperature to 350º F.

Step-By-Step Photos and Ingredients:

The muffin dry ingredients in a bowl with a whisk.

Step 1: Combine all of your dry ingredients in a large mixing bowl and whisk to blend the gluten free flour mixture.

The easiest way to measure your gluten free flour is to use either the spoon method or the leveling method.

Spoon Method: You can also use a spoon to fill the measuring cup. Use a knife to level along the top to remove the extra flour. Leveling Method: Fill the measuring scoop with flour, but do not pack it. Use a knife to scrape along the top to remove the extra flour.

The wet and dry muffin ingredients in a bowl about to get mixed.

Step 2: Add the wet ingredients to a separate bowl and whisk to blend. Pour the wet ingredients into the dry ingredients and mix gently.

📢 Sandi says: Every gluten-free flour blend has a different starch-to-grain ratio. The brand of gluten-free flour you use will affect the moisture of the batter. If your cake batter is too runny, add more flour, and if it is too thick, add more liquids.
Read Why Gluten-Free Flour Blends Vary to learn more about this.

The muffin batter in a muffin tin ready to bake.

Step 3: Scoop the gluten free muffin batter onto parchment paper muffin liners. Fill each cup of the muffin pan 3/4 full of the muffin batter.

Step 4: Bake at 350º F for 20-22 minutes until done. To test for doneness, insert a toothpick into the center of a muffin. If the toothpick comes out clean, it is done baking. If you see batter or crumbs, the muffins must be baked longer.

Step 5: Add powdered sugar and lemon juice to a small bowl. Mix them into the icing and drizzle the icing over the muffins. The whole family will love these muffins!

If you need more tips, be sure to check out my Gluten Free Muffins Troubleshooting Guide.

Frequently Asked Questions:

How do you know when the muffins are done baking?

The best way to test to see if your muffins are done baking is to insert a toothpick into the middle of a muffin. If the toothpick comes back clean, the muffins are finished baking. If you see batter or crumbs, the muffins must be baked longer.

Are poppy seeds safe to eat?

Poppy seeds have a bad rap, and many people worry about eating them. Unless you plan to eat several pounds of poppy seeds, the low amount of poppy seeds in baked goods and bagels will not affect you.

Can you freeze these muffins?

You can easily freeze these muffins. Allow them to cool completely, then add them gently to a large freezer bag. Seal it. To thaw your muffins, allow them to thaw slowly to room temperature on a plate or pop it into the microwave. If you use the microwave, the icing will get very hot, so be careful.

How do you store these muffins?

Store your muffins in an air-tight container in the refrigerator, or freeze them as instructed above. They will keep up to 4 days in the refrigerator or 4-5 months in the freezer.

A spoon drizzling icing over a lemon poppy seed muffin.

If you love lemons as much as we do, don’t miss the best gluten free lemon dessert recipes on the blog!

More Gluten Free Muffin Recipes to Try:

Reader Review:

Made these today! SO GOOD! Thank you for sharing this recipe! And I love all the non-wheat flours you use in the recipe! Fits with my allergy design! 🙂”


Love This Recipe?

If you made and enjoyed this recipe, I would be incredibly grateful if you could leave a comment below. Please include which flour blend you used. This will help others know this recipe is delicious. Thank you!

Gluten Free Lemon Poppy Seed Muffins

Sandi Gaertner
The best light and fluffy gluten free lemon poppy seed muffins recipe! They are perfect for breakfast or a snack.
4.85 from 20 votes
dairy free allergen icon
gluten free allergy icon
nut free allergen icon
soy free allergy icon
vegetarian icon
Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes
Course Gluten Free Breakfast Recipes, Gluten Free Muffins Recipes
Cuisine American
Servings 12 muffins
Calories 197 kcal


  • 1 ½ cups gluten free flour blend (See note)
  • 1 cup cane sugar
  • 1 teaspoon baking powder aluminum-free
  • ½ teaspoon baking soda
  • teaspoon salt
  • 1 tablespoon poppy seeds
  • ¾ cup non-dairy milk
  • 6 tablespoons lemon juice
  • 2 teaspoons lemon zest
  • 3 large eggs
  • ¼ cup coconut oil melted


  • ½ cup powdered sugar for icing
  • 1 tablespoon lemon juice for icing


  • Preheat the oven to 350º F.
  • In a large bowl, add the dry ingredients and whisk to blend.
  • In a bowl, add the wet ingredients and mix well.
  • Pour the wet ingredients into the dry ingredients and mix gently. (*See note)
  • Add the muffin batter to a muffin tray. Fill each about 3/4 full of the batter and bake for 22-25 minutes until done. (*See note)
  • Allow the muffins to cool on a cooling rack. Mix the lemon juice and powdered sugar to make the lemonade icing. Drizzle onto the muffins.


  1. If you prefer to use my custom flour blend to make these muffins, add 3/4 cup sorghum flour, 1/4 cup brown rice flour, 1/2 cup arrowroot starch (or tapioca starch), and 1 teaspoon Xanthan Gum to a bowl and whisk to blend.
  2. For the lightest and fluffy muffins, do not overmix them, or the muffins will not be as light and fluffy.
  3. To test whether your muffins are done baking, insert a toothpick into one. If the toothpick comes back clean, the muffins are done baking. If you see crumbs or batter, the muffins need to bake longer.
  4. These muffins will keep up to 4 days in an airtight container or up to 4 months in the freezer.


Please know that every gluten free flour blend has a different starch to grain ratio. If you use a blend I didn’t test, you may need to adjust your moisture levels in your baked goods.


Serving: 1gCalories: 197kcalCarbohydrates: 34gProtein: 3gFat: 7gSaturated Fat: 4gCholesterol: 41mgSodium: 107mgPotassium: 62mgFiber: 2gSugar: 22gVitamin A: 59IUVitamin C: 4mgCalcium: 60mgIron: 1mg
Tried this Recipe? Pin it for Later!Mention @FearlessDining or tag #FearlessDining!

Nutrition Disclaimer

Nutritional information is an estimate provided to you as a courtesy. You should calculate the actual nutritional information with the products and brands you are using with your preferred nutritional calculator.

This post was updated from an older June 2018 post with better directions and tips for success

4.85 from 20 votes (15 ratings without comment)

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating


  1. 5 stars
    Love this recipe! Made it today using Namaste flour as that is my go to flour. The muffins are light and tasty. I will certainly be making these again. Used my silicone muffin molds and baked for 22 minutes – nothing sticks.

  2. Hi there! I just made this recipe and the flavor and texture were great but the muffins really stuck to the muffin liners and I lost a lot of volume because of what remained stuck. They didn’t seem over cooked. Do you have a suggestion of what to adjust ?

    Thank you!

  3. Hello, quick question on this recipe. Is all of the lemon juice for the frosting? Or does some go in the muffins?

  4. Hi, I made these lemons and poppy seed muffins this morning and they did not turn out as per you photos. Please can you tell me where I went wrong.
    I follows your instructions using spoons and cups. I melted the coconut oil, was I supposed to let it cook completely before adding it? As this seems to be when things started to go wrong. As it hardened into lumps as I was storing it in. I tried to smooth the lumps out but the batter without over mixing. The batter was very runny, not thick like yours. Any ideas please? I love using new recipes but if I can’t find out where I went wrong I won’t be using this again. They haven’t really risen in the oven are have a very stodgy consistency. Thank you.

    1. Hi Lynne, what gluten free flour blend did you use? Some are starchy, and you need more flour than other blends. If you notice the batter is very runny, and doesn’t look like what I have posted in photos, you probably needed to add more gluten free flour.

  5. 5 stars
    Hi – tried this recipe and loved it! Planning to make several dozen for a school event next week. Have you had success in doubling or tripling the recipe as written?

  6. 5 stars
    Made these today! SO GOOD! Thank you for sharing this recipe! And I love all the non-wheat flours you use in the recipe! Fits with my allergy design! 🙂 I did make a couple changes due to allergies… almonds (used rice milk instead) and baking powder (upped the soda to 1-1/2 teaspoons). I also exchanged out the sugar with monk sugar 1:1 and threw in 1-1/2 cups blueberries. Incredibly yummy! Will make again….and again!

  7. 4 stars
    Not sure if i did something wrong but my muffins came out oily and treated somewhat oily. Note, my coconut oil is semi solid but melts on touch. I did melt it to ensure it was only 2/3 cup. Aside from that, favour was good though. Any suggestions?

    1. Hi Pete, I am so glad you messaged me about this. We chatted via FB and discovered that 1/3 cup worked better. Thank you so much.

    2. Any experience with coconut sugar?? I’m trying to lower and or elinate as much sugar as I can and don’t want to use artificial sugars. Love the sound of your lemon recipe but too much sugar!! Would love to know your thoughts on this.

      1. Hi Joy, I totally get that. I have not tested coconut sugar in this recipe, but I have used it in muffin recipes. I am thinking it will be fine to use, but note that your muffin color will be browner in color using coconut sugar.