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Gluten Free Lemon Poppy Seed Muffins

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This small batch of gluten free lemon poppy seed muffins are soft, moist, highlighted with fresh lemon, and dotted with crunchy poppy seeds.  The muffins are made with an almond blend plus a little sour cream to keep them moist.  Finished with a creamy citrus glaze, the muffins are great for breakfast, a light snack, or any time in between!

Close up bite shot of a super moist lemon breakfast muffin with a creamy glaze on a small cupcake stand.

Small Batch & Gluten Free Lemon Poppy Seed Muffins

This small batch recipe for lemon poppy seed gluten free muffins yields 4 soft and moist breakfast muffins.  The fluffy texture of the muffins gets a great contrast with the nutty crunch of poppy seeds.  And lets not forget the lemon – fresh lemon juice and zest add bright citrus flavor to the muffins.

I will say, my favorite part of these muffins is the creamy citrus glaze.  Which is slightly different than the lemon glaze on the gluten free lemon loaf.   We use coconut milk to make this glaze extra creamy and smooth.

Why You’ll Love These Muffins

  • Soft – The combination of gluten free flours – almond, sweet rice flour, and tapioca flour – make the muffins fluffy and soft.
  • Moist – We use sour cream to make the muffins moist.  Similar to my gluten free blueberry muffins, gluten free chocolate chip muffins, and traditional chocolate chip muffins recipes.
  • Bursting with Lemon – Fresh lemon juice and zest ensure the citrus notes shine in these muffins.
  • Crunchy Poppy Seeds – The nutty poppy seeds provide a fun bite to the muffins.
  • Creamy Muffin Glaze – Like the orange glaze in my almond orange scones, this glaze can easily be served in a small bowl next to the muffins for a little dunking action!  
  • Easy Recipe – The nature of small batch and un-fussy ingredients make this an easy muffin recipe.
A small batch of gluten free lemon poppyseed muffins arranged on a wire rack.

What You Need To Make A Small Batch Of Lemon Poppy Seed Gluten Free Muffins


  • Almond Flour – I use blanched almond flour because it is ground finer and without the almond skins, and is the base for all my gluten free recipes.  Almond flour provides structure, flavor, and moisture.
  • Sweet Rice Flour – Sweet rice flour adds moisture and binding properties.
  • Tapioca Flour – The tapioca flour adds a little chew and makes the muffins soft.
  • Coconut Flour – Coconut flour is wonderfully absorbent and I like to use to balance all of the wet ingredients.
  • Baking Powder – To achieve muffin loft and texture.
  • Salt – Salt balances and enhances flavor.
  • Poppy Seeds – Without poppy seeds, these aren’t lemon poppyseed muffins!
  • Sugar – I use organic cane sugar because it isn’t as processed and refined as regular sugar.  Though, you can use granulated sugar if you prefer.
  • Coconut Oil– I like to use coconut oil to keep the muffins moist longer.  You can use melted butter – just note the muffins may only stay moist for about 1 to 2 days.
  • Sour Cream – Sour cream acts as a moisture provider for the muffins.
  • Egg – Just one egg!
  • Vanilla Extract – For a little extra flavor.
  • Lemons – 2 small lemons for the muffins and glaze.

Baking Equipment

  • Mixing Bowls
  • Muffin Pan with Liners

Creamy Citrus Glaze For Muffins

I love it when muffins have a little extra something.  Heck, I love it when any sweet treat has a little something extra!  But, when it comes to muffins, I feel bad because they don’t inherently come with frosting like cupcakes.  

Not these muffins though!  We are giving them a delicious topping that can stay as a topping, or easily smeared on the muffin like butter.  And this deliciousness comes together with 3 ingredients:

  • Lemon – The juice and zest.
  • Coconut Cream – From a can of unsweetened coconut milk.  Creamy glaze needs a creamy base.
  • Powdered Sugar – For sweetness, and the powdered sugar will help the glaze thicken.

The glaze can be spread over the top of cool muffins.  Or, if you’re like me, spackled on to each bite!

Creamy lemon glaze ingredients in small white bowls arranged on a table.

Tips For Success

  • Use fresh lemons – For the juice and the zest.  The strong lemon flavor actually comes mostly from the zest.  Without it, you may not be able to tell these are lemon muffins.
  • Full fat sour cream – I like the fat content to keep the muffins soft and moist.  I have had success using yogurt in my gluten free chocolate chip muffins.  But I prefer the heft sour cream adds to muffins.
  • Let the batter rest before baking – This allows the flour (specifically sweet rice flour) to hydrate.  Otherwise, the muffins may be a bit crumbly if you don’t give the batter time to rest.
  • Refrigerate the can of coconut milk overnight – This will make the cream and liquid separate in the can.  We are only using the cream in the can.
  • Use leftover coconut cream for smoothies or whipped cream – You will have leftovers.  The coconut milk is great in fruit smoothies or to make a small batch of whipped coconut cream.
  • Let the muffins cool completely – For two reasons:  they taste better when they have had a chance to cool.  And the creamy glaze won’t melt into the muffins!
Two gluten free lemon poppyseed muffins stacked on a wire cooling rack.
A single gluten free lemon breakfast muffin with lemon cream glaze set on a small cupcake stand.

FAQ’s: Gluten Free Lemon Poppy Seed Muffins

Can this small batch recipe be doubled?

I have not tested a larger batch, but if you try let me know how they turn out!

Why 2 lemons for a small batch muffin recipe?

I like to use organic lemons, which tend to be smaller. Additionally, we use lemon juice and zest for the muffins and glaze.

Can I use refrigerated or pre-made lemon juice?

You can, but the muffins won’t have the same lemon flavor. We achieve the strong lemon flavor from the zest. And I don’t recommend adding extra lemon juice to the muffins as it will alter the outcome.

Will a 1:1 gluten free flour work?

Likely not. I have not tested it for this recipe, but I will say that I find the 1:1 blends to be drier. Therefore, other ingredient ratios may need to be adjusted.

Can I use yogurt instead of sour cream?

You can, but keep in mind yogurt doesn’t have the same fat content as sour cream. The muffins may not be as moist.

Does the creamy glaze set up hard?

Not as it is written. You can have it set firmer by using more powdered sugar.

How do I store baked muffins?

Un-glazed muffins will stay soft and moist for about 2 days covered at room temperature. Add the creamy glaze when you’re ready to serve.

How do I store the creamy glaze?

The glaze should be stored in a covered container in the refrigerator.

Can I freeze the baked muffins?

Yes. Freeze un-glazed muffins in a tightly wrapped/sealed container or plastic wrap for up to 3 months. Thaw in the refrigerator then bring to room temperature for serving.

Bite shot of a moist gluten free lemon poppyseed muffin with lemon cream glaze on a white plate.
Close up bite shot of a super moist lemon breakfast muffin with a creamy glaze on a small cupcake stand.
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5 from 2 reviews

Gluten Free Lemon Poppy Seed Muffins

Yield: 4 Muffins
This small batch of gluten free lemon poppy seed muffins are soft, moist, highlighted with fresh lemon, and dotted with crunchy poppy seeds.  The muffins are made with an almond blend plus a little sour cream to keep them moist.  Finished with a creamy citrus glaze, the muffins are great for breakfast, a light snack, or any time in between!
Prep22 minutes
Cook15 minutes
Total37 minutes



  • 2 small lemons

Gluten Free Lemon Poppy Seed Muffins

Creamy Lemon Glaze


Gluten Free Lemon Poppy Seed Muffins

  • Preheat the oven to 350F degrees and adjust the oven rack to the middle position. Line a muffin pan with 4 cupcake liners.
  • In a small mixing bowl, whisk together the almond flour, sweet rice flour, tapioca flour, coconut flour, baking powder, salt, and poppy seeds.
    1/4 cup, plus 1 tablespoon blanched almond flour, 3 ½ tablespoons sweet rice flour, 1 tablespoon tapioca flour, 1 tablespoon coconut flour, 1/2 teaspoon baking powder, 1/4 teaspoon salt, 2 teaspoons poppy seeds
  • In a medium mixing bowl, add the sugar, sour cream, coconut oil, egg, vanilla, lemon juice, and lemon zest. Whisk until incorporated and smooth.
    1/4 cup organic cane sugar, 2 tablespoons full fat sour cream, room temperature, 1 tablespoon cold pressed refined coconut oil, melted, 1 large egg, room temperature, 1/2 teaspoon vanilla extract, 2 teaspoons lemon juice, 2 teaspoons lemon zest
  • Lemon Notes – Depending on the size of your lemons, you may need one entire lemon for the zest. Additionally, add more or less lemon zest if you prefer a strong lemon flavor. However, do not add more lemon juice than noted – otherwise it will change the texture of the muffins.
    2 small lemons
  • Sprinkle the dry ingredients over the wet, and stir until no dry streaks remain.
  • Scoop the batter into equal portions into the prepared muffin liners. The liners will be about 90 percent full. Let the muffins sit for 5 minutes before baking to give the batter time to hydrate. Otherwise, the muffins may turn out crumbly. Bake the muffins for 20 to 22 minutes, or until the edges are golden, the muffins are springy to the touch, and a toothpick inserted in the middle comes out mostly clean.
  • Cool the muffins in the pan set on a wire cooling rack for 10 minutes. Then transfer the muffins to the wire rack to cool completely. While the muffins are cooling, make the creamy glaze.

Creamy Lemon Glaze

  • We are only using the coconut solids from the can. For best results, refrigerate the can of coconut milk overnight so the coconut solids and liquid separate in the can.
  • In a small mixing bowl, add the creamy coconut, powdered sugar, salt, and lemon zest. Stir until smooth and creamy. You can also use a hand held mixer to mix if the coconut solids are lumpy. See the note in the muffin instructions for amount of lemon zest.
    1/4 cup unsweetened canned coconut milk or cream, full fat, 3 to 4 tablespoons powdered sugar, pinch salt, 2 teaspoons lemon zest
  • Taste the glaze. For more lemon flavor, add the lemon juice in 1 teaspoon increments. Adjust the consistency of the creamy glaze to your preference by adding more powdered sugar for thicker, or more lemon juice for thinner. The creamy glaze is intended to be creamy, but feel free to make it your own.
    1 to 2 teaspoons lemon juice
  • Spoon the glaze over the top of completely cool muffins, and Enjoy!
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  • Serving Size – This recipe is intended to be a small batch and only tested as such.  I can’t say for certain if doubling the recipe will yield the same result.
  • Ingredient Substitutions – I have only tested the recipe as written.  
  • Poppy Seeds – Poppy seeds are available in the spice aisle of your grocery, or you can buy them online.
  • Lemons – I like to use organic lemons because we are using the zest.  They also tend to be smaller.  1 small lemon will likely yield 2 teaspoons of zest.
  • Lemon Flavor – For the muffins – if you prefer a strong lemon flavor, use more zest.  More juice will alter the muffin texture.  For the glaze – taste as you go and add more zest or juice as needed.
  • Creamy Lemon Glaze – The glaze is intended to be creamy – it will not dry hard.  If you prefer a hard lemon glaze, only use about 3 to 4 teaspoons of the coconut cream.  Add more if needed to reach your desired consistency.  
  • Leftover Coconut Milk – You will have leftovers.  It can be used in fruit smoothies, to make overnight oats, or whipped coconut cream.
Course: Breakfast
Cuisine: American
Author: Erin Cernich


Calories: 309kcal | Carbohydrates: 37g | Protein: 7g | Fat: 17g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 0.01g | Cholesterol: 50mg | Sodium: 226mg | Potassium: 158mg | Fiber: 4g | Sugar: 21g | Vitamin A: 118IU | Vitamin C: 33mg | Calcium: 117mg | Iron: 2mg
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
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