Gluten-Free Lemon Poppy Seed Muffins

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Gluten-Free Lemon Poppy Seed Muffins – These bright, sunny gluten-free lemon muffins are a total DREAM! Fluffy and citrusy with every bite. (Dairy-Free)

Front view of gluten-free lemon poppy seed muffins cooling on a cooling rack

Can we just talk about how delicious lemon poppy seed muffins are? They’re one of my ALL-TIME favorite muffins. They’re so sunny and bright!

I’m a stickler with my lemon baked goods, and when I tell you I made more than a dozen versions of these muffins before they were just right, I mean it!

Our gluten-free lemon poppyseed muffins were 100% worth the wait. They’re light & fluffy, and they’re bursting with lemon flavor in every bite. I’m spilling all our secrets for getting the most lemon flavor in your muffins, and I think once you taste them, you’ll never go back.

Here’s what you’ll need to get started on this easy recipe…

Simple Ingredients For Gluten-Free Lemon Poppy Seed Muffins:

For The Wet Ingredients:

  • Lots Of Fresh Lemon Zest. This is crucial for getting that fresh, bright lemon flavor! You’ll use 2 1/2 tablespoons, which is about 3 lemons’ worth of zest. It’ll look like a lot, but it’ll taste *just* right!
  • Sugar. To sweeten these muffins, we’re using regular sugar. I don’t recommend swaps or substitutions here. We tried them with honey and pure maple syrup, and neither tasted as lemony as when we used regular sugar.
  • Avocado oil. You can really use any favorite neutral-tasting oil here, like sunflower oil, grapeseed oil, vegetable oil, or canola oil. I don’t recommend coconut oil, as it impacts the flavor.
  • Eggs. These give puff and stretch to the muffins.
  • Milk & Fresh Lemon Juice. I use unsweetened almond milk when I make these lemon poppy seed muffins, but you can use whatever milk you drink (dairy milk, soy milk, cashew milk, etc.). Then, we add lemon juice for acidity & flavor.
  • Vanilla & Almond Extract. It might sound strange, but we made test batches with and without almond extract and the ones with almond extract had a stronger lemon flavor! Its sweet notes really highlight the lemon!
  • Lemon Oil (Or Lemon Extract). I highly recommend lemon oil if it’s at all possible for you! It’s got the most concentrated, fresh lemon flavor. If you can’t find it or it doesn’t fit the budget, I do recommend lemon extract. We’re using just enough for brightness, but not so much that it’ll taste artificial.

For The Dry Ingredients:

  • Gluten-Free Measure-For-Measure Flour. We recommend our favorite King Arthur Measure For Measure Flour blend (not sponsored, just love it!). It gives great texture to muffins, cookies, brownies, cakes, and more. Also know that you CANNOT swap for almond flour or coconut flour here.
  • Poppy Seeds. They wouldn’t be gluten-free lemon poppy seed muffins without poppy seeds, right?
  • Baking Powder. For lift and puff. You’ll love the rise on these glorious gluten-free lemon muffins!
  • Salt. Balance those flavors!

3 Tricks For Getting More Lemon Flavor In Your Lemon Poppy Seed Muffins:

1. Rub The Zest Into The Sugar First!

Using lemon zest is a great way to add fresh lemon flavor to these easy lemon poppy seed muffins and other lemon baked goods, but you can unlock even MORE of that lemon flavor by rubbing the lemon zest into the sugar before you begin. This releases the lemon essential oils from the zest and distributes it over the granules of sugar. Instead of all the lemon flavor being concentrated in the zest only, it’s now in every single bite thanks to the zest & the lemon zest-infused sugar!

2. Add Lemon Juice.

In addition to the fresh lemon zest (a MUST for these fluffy muffins!), we’re also adding some fresh lemon juice. I only recommend fresh lemon juice here, since you’ll already have fresh lemons on hand for the zest. Bottled lemon juice can get bitter and acidic, while fresh has a much brighter, more balanced flavor.

3. Use Lemon Oil Instead Of Lemon Extract.

Last but not least, I recommend using lemon oil instead of lemon extract. You do need to use one of the two in this recipe if you really want the lemon flavor to shine, and lemon oil will give you the freshest, most concentrated lemon flavor. It’s not something most people have lying around in their kitchen, but if you like lemon baked goods (cakes, muffins, etc.), it’s definitely worth keeping on hand! Use culinary lemon oil (best choice!), or food-grade essential oil (second best choice). Do NOT use aromatherapy oils! Note that because it’s more concentrated, you need LESS lemon oil than lemon extract.

A soft, fluffy gluten-free lemon poppy seed muffin

FAQ + Tips For The Best Gluten-Free Lemon Poppy Seed Muffins

The BEST Muffin Liners EVER! I *hate* it when half of my muffin sticks to the muffin liner! I never have that problem with these parchment muffin liners. They’re the most nonstick liners I’ve ever tried. I almost exclusively use them almost for muffins and cupcakes. While you’re at it, use a light-colored muffin pan for more even baking. (Dark pans brown too quickly and can burn)

Try A Cookie Scoop For Portioning Batter! I use cookie scoops for All The Things, but one of my favorite (besides cookies, obvs) is for portioning muffin batter or cupcake batter into the pan. It makes it so much easier to make them all equal! I use my large cookie scoop for this job most of the time, but if I could only own one scoop, it’d be the medium size.

Can You Freeze Lemon Poppy Seed Muffins? You bet! If you want to freeze your gluten-free lemon poppy seed muffins, let them cool all the way to room temperature, then transfer to an airtight, freezer-safe bag and store in the freezer 4-6 weeks.

Can I Make Lemon Poppy Seed Muffins With Almond Flour or Coconut Flour Instead? No! Not for this recipe. The formulation of wet/dry ingredients is calculated based on gluten-free measure for measure flour and will not work with almond or coconut flours. If you need an almond flour lemon poppy seed muffin recipe, One Lovely Life has a great one!

Pouring lemon glaze on gluten-free lemon poppyseed muffins

More Gluten-Free breakfast recipes to love:

WE ♥

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Front view of gluten-free lemon poppy seed muffins cooling on a cooling rack

Gluten-Free Lemon Poppy Seed Muffins

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  • Author: Sweets And Thank You
  • Total Time: 35 minutes
  • Yield: 12 Muffins 1x
  • Diet: Gluten Free


These bright, sunny gluten-free lemon muffins are a total DREAM! Fluffy and citrusy with every bite. (Dairy-Free)



For The Wet Ingredients:

  • 2 1/2 Tbsp. lemon zest (from 3 lemons–don’t skimp!!!)
  • 1 cup sugar
  • 2/3 cup avocado oil (or your favorite neutral oil, like sunflower, grapeseed, or canola)
  • 2/3 cup milk (I use unsweetened almond milk)
  • 2 Tbsp. fresh lemon juice
  • 3 eggs, room temperature
  • 1/2 tsp. vanilla extract
  • 1/2 tsp. almond extract
  • 1/4 tsp. lemon oil (or 1/2 tsp. lemon extract. Note that lemon oil will give you stronger flavor!)

For The Dry Ingredients:

  • 2 cups (240g.) gluten-free measure for measure flour, scooped & leveled or weighed (we recommend King Arthur brand)
  • 2 Tbsp. poppy seeds
  • 1 1/2 tsp. baking powder
  • 1/2 tsp. salt


To Make The Gluten-Free Lemon Poppy Seed Muffins:

  1. Preheat the oven to 350 degrees F. Line a 12-cup metal muffin pan with parchment muffin liners.
  2. First, start by combining the lemon zest and sugar in a large mixing bowl. Rub the zest into the sugar with your fingertips for 30-60 seconds until the sugar smells bright and lemony and the sugar has taken on a yellow appearance.  (Rubbing the zest into the sugar releases the lemon essential oils from the zest and distributes them further in the recipe. This = more lemon flavor!)
  3. Next, add the oil to the sugar/zest and whisk to combine. Add milk and lemon juice and whisk to combine.
  4. Then add eggs, vanilla, almond extract, and lemon extract/oil and whisk to combine.
  5. Add gluten-free flour, poppy seeds, baking powder and salt. 
  6. Stir until just combined and no large lumps of flour remain. 
  7. Scoop the batter into your prepared muffin tin, filling each muffin cup almost all the way full. (Update: for best results, let the batter rest 30-60 minutes for a taller rise!)
  8. Bake muffins at 350 degrees F. for 17-20 minutes, or until the tops spring back when you gently press down and a toothpick inserted in the center comes out clean with just a few moist crumbs. 
  9. Cool on a wire rack and enjoy plain or cool completely and top with lemon glaze. Store leftover muffins in an airtight container up to 3 days or freeze up to 2 months. 


*Stick To The Recipe! I know it’s tempting to put your own spin on a recipe, but any omissions or substitutions you make here will mess with the flavor. Don’t skip the almond extract, lemon zest, or lemon oil/extract. Each one adds a layer of flavor you NEED for these lemon muffins to work properly. 

*We highly recommend King Arthur Measure-For-Measure Gluten-Free flour for these muffins. If you use another brand (like Bob’s Red Mill), just be sure it contains xanthan gum. Measure carefully! 

  • Prep Time: 15 minutes
  • Cook Time: 18 minutes
  • Category: Muffins
  • Method: Baking
  • Cuisine: American
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