Gluten free lemon poppy seed muffins

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Last Updated on December 7, 2023

These gluten free lemon poppy seed muffins are the best. They’re perfect for gluten-free baking and loaded with lemon flavor. Who knew that muffins made with gluten-free flour could taste this good? If you’re in the market for a muffin recipe made with fresh lemon and other simple ingredients, you’re going to want to make this recipe today!

close up of Gluten free lemon poppy seed muffins

Growing up, I had been looking for a delicious lemon poppy seed recipe for a long time. In fact, I didn’t have a muffin until I was a teenager.  My Filipina mother had no idea what a muffin was at the time but somehow we finally managed to get her to buy some Lemon Poppy Seed Muffins from the bakery in the commissary.

Please believe my sisters, brother and I demolished that package in 2 seconds flat.  I barely remember the flavor only that it was good and sweet.  I had forgotten about this recipe but I’m so glad I was able to piece it together again.  The flavor and texture remind me of that first time all over again.

The first time you take a bite of a truly delicious gluten free lemon poppyseed muffin, you’re never going to forget that flavor and taste. The added lemon zest make these muffins the perfect citrus flavor!

This is one of those gluten-free recipes that you’re never going to forget – and now that you’re going to find out how to make your very own gluten-free lemon poppy seed muffins, you’re not going to have to.

paleo lemon poppy seed muffins Gluten Free

Can you add any toppings to these gluten free lemon poppy seed muffins?

You can literally change up this lemon poppyseed muffins to fit whatever flavor and tastes you like. Just be sure that whatever you use, it’s free of gluten as well. Using the lemon zest to make a nice lemon glaze is always a good idea. The great thing about adding toppings to a poppy seed muffin is that you have options!

Another popular topping that is simple is powdered sugar. Just sprinkle on the powdered sugar, and you’re good to go. There’s just something about the sugar and lemon combination that are stellar together.

Make sure that you let the muffins cool completely before adding on any type of glaze or topping. If you mix and add to early, the glaze will literally melt right off.

Why You’ll Love These Gluten Free Lemon Poppyseed Muffins

  • This paleo muffin is so moist with the perfect hint of sweet and lemon.  (I ate three and thankfully my son and husband polished off the rest.)  
  • You can bake this directly in your muffin tin.  To do this simply grease the pan well and reduce the cooking time by 5 minutes.
  • These gluten free lemon poppy seed muffins are some of the best baked goods!

Ingredients Needed to Make Lemon Poppy seed muffins

  • coconut flour (or any gluten free flour)
  • poppy seeds
  • baking soda
  • coconut oil, melted
  • honey
  • pure vanilla extract
  • lemon
  • eggs
  • milk of choice, almond, coconut, etc

How To Make gluten free lemon poppy seed muffins

  1. In a small bowl combine the coconut flour, baking soda and poppy seeds.
  2. In a small pan on your stove top, melt the coconut oil. Next, add in the lemon juice and rind and keep warm for 1 minute to help release the oils from the rind.
  3. Then add in the vanilla and honey and let cool.
  4. Lastly, add the milk and eggs to the liquid mixture and combine them with the dry ingredients.
  5. Pour the batter into muffins tins and bake at 325 for 20 – 25 minutes.

Tips for Making lemon poppy seed muffins

  • Don’t over stir the muffin batter. Just add and stir until combined.
  • Get the muffins to cool by sitting them on a wire rack.
  • These lemon poppy seed muffins can be split to have powdered sugar on some, lemon glaze on some, and some served up as is.
  • If you want to add more lemon zest, go for it. Some people prefer a stronger lemon flavoring than others.

Can you make this muffin recipe without the poppy seeds?

Technically, you can but then you wouldn’t have lemon poppy seed muffins! But yes, if you want that flavor and aren’t a fan of adding in poppy seeds, you can still make gluten free lemon muffins without them!

How do you know when these gluten free lemon poppy seed muffins are done baking?

The easiest way to tell if your poppy seed muffin pan is ready to pull from the oven is to do the toothpick test. Put a clean toothpick into the middle of one of the muffins, then remove it. If there is no muffin batter on the toothpick, the gluten free lemon poppyseed muffins are done and ready to taken out of the oven and set aside.

How do I store leftover gluten free lemon poppyseed muffins?

To store leftover muffins, just let them cool down to room temperature and store them in an airtight container. This recipe doesn’t have to be stored in the fridge and can be left at room temperature if you’d like. It’s really up to you.

I do think that storing muffins in the fridge will keep them fresh for just a little bit longer.

Where can I buy poppy seeds?

Head to the local grocery store to buy your poppy seeds. More than likely they’ll have them in the nut section, or the spices section of the store. Don’t start making your muffins until you have all the ingredients on hand!

Can I use lemon juice instead of real lemons to get that lemon flavor?

You can. If you only have lemon juice, just use it. To be honest, if you use the lemon juice in the muffins or the lemon glaze, you might not even be able to tell a huge difference. Lemon juice typically doesn’t have any artificial additions so using lemon juice should work out just fine for your poppy seed muffin recipe.

The next time that you’re in the mood for gluten free baking, these muffins are perfect! No matter if you use a fresh lemon or opt to flavor your muffin with lemon juice, this recipe isn’t going to disappoint! Treat yourself to some of the best gluten free muffins without having to worry about anything else!

When you have gluten free recipes that are simple and easy like this one, it’s one recipe that you’re going to want to mix and make over and over again! Luckily the prep time and cook time are low and the flavor of this recipe is high!

Paleo Muffin Poppy Seed Gluten Free
Yield: 9

Gluten free Lemon Poppy Seed Muffins

Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes

These gluten free lemon poppy seed muffins are easy to make and they're delicious. They're perfect for breakfast, brunch, or a snack!


  • 1/2 cup coconut flour
  • 1 tablespoon poppy seeds
  • 1/2 tsp baking soda
  • 1/3 cup coconut oil, melted
  • 1/4 cup honey
  • 1/2 teaspoon pure vanilla extract
  • cup Juice of 1 medium lemon, about 1/4 and zest the rind, about 1 1/2 tbsp
  • 3 eggs
  • 1/2 cup milk of choice, almond, coconut, etc


  1. In a small bowl combine the coconut flour, baking soda and poppy seeds.
  2. In a small pan on your stove top, melt the coconut oil. Next add in the lemon juice and rind and keep warm for 1 minute to help release the oils from the rind.
  3. Then add in the vanilla and honey and let cool.
  4. Lastly add the milk and eggs to the liquid mixture and combine with the dry ingredients.
  5. Pour the batter into muffins tins and bake at 325 for 20 - 25 mnutes.

Did you make this recipe?

Please leave a comment on the blog or share a photo on Instagram

gluten free lemon poppy seed muffing with a bite missing

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59 thoughts on “Gluten free lemon poppy seed muffins”

  1. I was probably in high school when I had a muffin–my mom never made them and certainly would not have purchased anything prepackaged! Your Paleo Muffins look fabulous, momma!

  2. Delicious and fluffy! I made these but messed up with the coconut oil and it hardened in chunks when i added eggs (I’ll probably leave the eggs and milk out so they get up to room temp next time) so I threw all the liquids into the blender for two minutes and it all worked out, and perhaps made them even fluffier!
    Rating this five stars, it deserves it. Excellent recipe.

  3. Thank you! I used the coconut milk. The muffins are very attractive. They are kind of wet on the inside but I’m used to that when baking with coconut flour. I knew with only 1/4 cup honey they wouldn’t be too sweet (that’s what I liked about the recipe) but they had a bitter taste to them. =( I don’t know if I had a bad lemon or what but I’m disappointed. What do you think I did wrong?

    • Hrmm. . . bitter? It may have been the lemon or goodness, I don’t know maybe the coconut milk. Does the brand you use have any additives in it? Maybe there was a strange reaction? I’ll add this to my list of tutorial videos.

  4. I will admit I am new to Paleo baking and have tried Paleo muffins that call for coconut flour, with MORE than disappointing results. I have not tried these beauties yet, but they look VERY MUCH like wheat flour based lemon poppyseed muffins, so flully with a great crumb!

    I have read recently in my exhausting web search for everything Paleo cooking that tapioca flour/starch adds more of the flakiness/rise/texture of wheat flour muffins. Do you ever use this, and, if so, is there any “formula” for how much and when, and if you sub out some of the flour called for in the recipe for the tapioca? I’m trying these in the morning!! Thanks for the help – beautiful site!! Jennie

    • Thanks Jennie. I do use tapioca flour but, hrmm .. I can’t think of an easy way to break down baking with it. I have not tried it in muffins yet but I do have a cinnamon roll recipes that is fantastic made with it and coconut flour. Sorry that doesn’t help!

  5. I’m really excited to try these! But I’m having a frustrating time trying to screenshot the recipe on my ipad & phone before a million pop ups appear that I can’t get rid of πŸ™

  6. Thank you for this amazing recipe! These came out perfect! I am going to experiment making this into a cake, tripling the recipe for a double layer and making a lemon coconut cream frosting. Wish me luck;)


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