Gluten Free Lemon Poppy Seed Muffins

Moist and fluffy, these Gluten Free Lemon Poppy Seed Muffins are the best Lemon Muffins there are. Made with lots of lemon zest and poppy seeds and finished with a simple lemon glaze made with fresh lemon juice. Which you should not skip - it really takes this recipe to the next level.

These gluten free lemon muffins are perfect for your morning coffee or your next brunch get together. Everyone will love them.

Recipe Ingredient Notes

Gluten Free Flour: I have tested this recipe for gluten-free lemon poppy seed muffins with my own gluten-free flour blend and Bob's Red Mill 1-to-1. Both flour blends produced a tender, moist crumb and exceptional flavor. I am not saying other brands will not work in this recipe. I just have not tested them in this application. Flour blends used to develop this do contain xanthan gum.

Almond Flour: Gluten Free Muffins tend to have a very blah structure and crumb - this is why I love adding almond flour to the dry mix. Make sure to use Almond Flour since Almond Meal tends to have a coarse texture. If you prefer to keep this recipe nut-free, please substitute the almond flour with the same amount of gluten-free flour. 

Lemons: Since we are using the zest of the lemons in this recipe for lemon muffins recommend using organic lemons (if you can). No matter what, make sure to give them a good rinse.

Neutral Oil: I recommend using a neutral oil such as grapeseed oil or mild olive oil in this easy recipe. Coconut Oil has a strong flavor and overpowers the lemon flavor. The added oil keeps the muffins moist (while the butter provides the flavor and structure)

Poppyseeds: Can't make lemon poppy seed muffins without poppy seeds. Poppy seeds come from the same plant that produces opiates, including morphine and codeine. Poppy plant cannot be legally grown in the US, all poppy seeds available in this country are imported from countries where cultivation is allowed.

How to make Gluten-Free Lemon Poppyseed Muffins

The beauty of this gluten-free lemon muffin recipe is the fact that the eggs, sour cream (or greek yogurt), buttermilk, and unsalted butter don't need to come to room temperature or be melted. So no need to wait around before you can start baking.

This recipe will make 12-16 gluten-free muffins depending on how full you fill the cavities. Since I do have multiple muffin pans, I scoop all the muffins at once BUT only bake one muffin tin at a time. The second pan will rest in the fridge until it is turn. The smaller you make the muffins, the faster they will bake. So keep this in mind when making this recipe.

Like all my other gluten-free muffin recipes, these muffins benefit from a 20-30 minute chill prior to baking.

Step 1: Line your muffin pan with 12 muffin liners and set aside. These liners are sometimes called Muffin Cups or Cupcake liners. This recipe will make 12-16 muffins.

Step 2: In the bowl of the stand mixer fitted with the paddle attachment combine the granulated sugar and the zest of two lemons. With clean fingers work the lemon zest into the sugar. This will release the oils and lemon flavor found in the zest.

Step 3: Add the gluten-free flour, almond flour, baking powder, baking soda, kosher salt, and poppy seeds to the granulated white sugar and whisk to combine.

Step 4: To a separate large mixing bowl add the buttermilk, vegetable oil, sour cream, large eggs and pure vanilla extract. With a whisk, combine the wet ingredients until smooth and no lumps remain. Set aside.

Step 5: Cut the cold, unsalted butter into smaller pieces and add to the dry ingredients. Mix at a low speed until it resembles a mealy powder and the big chunks of butter are the size of lentils. It is okay if there are some visible small chunks of butter.

Step 6: Add the wet ingredients to the dry ingredients and mix at a medium-low speed until a batter forms. There may will be some visible chunks of butter but that's nothing to worry about.

Step 7: Using a large cookie scoop (like this #20 scoop) fill each cup with batter all the way to the top. If you only have one muffin pan, you can allow the remaining muffin batter to sit in the mixing bowl and place it in the fridge.

Step 8: Place the gluten-free muffins in the fridge while your oven preheats to 350F. Even if it’s just 15-30 minutes will help hydrate the flour which builds a better crumb. Also – cold muffin batter will rise higher and give them a bakery style muffin top.

At this point, you can store the lemon poppyseed muffin batter in your fridge for up to 3 days. I like to just go ahead and scoop them into the muffin tins and carefully cover them with foil. When I am ready to bake, I don't have to wait around and can pop them right into the preheated oven.

Homemade Lemon Syrup

This homemade lemon syrup is super simple to make and gives the lemon muffins, even more lemon flavor. I don't recommend skipping this since it really makes the recipe. One can make this lemon glaze ahead ahead of time and store in the fridge up to 3 months. It's not only perfect to enhance the lemon flavor of this recipe but also my Gluten Free Lemon Bundt Cake and Gluten Free Lemon Loaf.

Step 1: To make this simple lemon syrup, combine the juice from fresh lemons and granulated sugar in a small saucepan. Bring to a simmer and allow to cook until the sugar is dissolved. This will only take a few minutes.

Step 2: Remove the lemon syrup from heat and add some additional lemon zest. (Make sure to zest the lemon BEFORE juicing it). This will bring out even more lemon flavor. Allow to cool while the Lemon Poppy Seed Muffins are baking.

How to bake Gluten Free Lemon Muffins

Step 1: When ready to bake the gluten free lemon poppy seed muffins and the oven is fully preheated to 350F, place the muffin tin in the oven.

Step 2: Bake the lemon muffins at 350F for 25-27 minutes one pan at a time until they are golden brown. I always check the doneness after 25 minutes. The muffins are done when until they are golden brown and a toothpick inserted in the center comes out clean. Make sure not to overbake them. That will cause them to dry out. If using a digital thermometer, the internal temperature should be 200F.

Step 3: Remove the muffin pan from the oven and place on a wire rack. While still hot brush them with a generous amount of the lemon syrup.

Step 4: Allow the gluten free lemon poppy seed muffins to cool in the muffin pan for 5 minutes before carefully removing them to a cooling rack to cool completely. If you allow them to cool completely in the muffin tin, the heat can't escape and the muffin papers will be soggy.

Repeat the baking process with the remaining gluten-free muffin batter.

Storage & Freezing

These muffins are the best the day they have been baked - especially if they are still warm from the oven. But they can be store at room temperature in an airtight container up to 3 days. Should they become soggy, place a piece of paper towles on the bottom of your container. Top them with another piece. The paper towels will act as a sponge and will absorb moisture.

To freeze the gluten-free muffins, place them on a sheet tray. Pop them in the freezer for 30-45 minutes or until they are solid. Once frozen transfer them to an airtight container or freezer bag. Freeze up to 3 months. When ready to eat, allow for them to thaw at room temperature or nuke in the microwave for 15-30 seconds.

FAQ about Lemon Poppy Seed Muffins

Note about Salt in my Recipes

I use Diamond Kosher Crystal Salt in all of my recipes unless otherwise stated. If use use a different brand or kind of salt in your kitchen please adjust accordingly since some salts can be saltier. If you use Morton’s Kosher Salt please be aware that their salt granules are smaller in size, denser, and crunchier and twice as salty.

Baking in grams

I share my recipes in grams and by weight since baking by weight is the most accurate way to bake. Digital Scales are very affordable and easy to use. You can purchase them on Amazon for less than a set of measuring cups. For small amounts under 10 grams, I like to use this Precision Pocket Scale. Measuring cups are very inaccurate which can cause significant errors when it comes to gluten-free baking or baking in general. Especially since I bake with gluten-free flours which weigh differently than “regular” flours. I do provide some ingredients like spices and leavening agents in measuring spoons. To learn more about Baking with a digital scale, make sure to check out my post about Baking by weight.

Note about Ovens and Oven Temperatures

All my recipes are tested and developed with a conventional oven. I always bake my baked goods on the rack placed in the MIDDLE of my oven. This way the heat coming from the bottom will not burn my baked goods.

If you are baking with convection (fan-forced), please adjust the recipes accordingly. Convection oven can cause baked goods to dry out quickly and still be raw inside. Since takes at least 15-20 minutes for a standard American Oven to be fully preheated. I highly recommend investing in an Oven Thermometer.

Substitutions and Modifications

Any dietary or ingredient modifications/substitutions to this recipe may alter the end result in appearance and taste. I test my recipes several times as published in this post and The Gluten Free Austrian Blog is not responsible for the outcome of any recipe you find on our website.