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Gluten Free Lemon Poppy Seed Muffins

These gluten free lemon poppy seed muffins are sweet and fragrant with lemon and balanced by crunchy poppy seeds scattered throughout. Oat flour and almond flour combine to create a sturdy yet tender crumb that’s beautifully gluten free.

A gluten free lemon poppyseed muffin is cut in half on a plate with more muffins in the background.

Gluten Free Lemon Poppy Seed Muffins Recipe

Lemon is one of my favorite ingredients to tuck into everything from a snacking cake to a quick bread or a sweet and simple bundt cake. In these gorgeously simple lemon poppy seed muffins, the classic combination of lemon and poppy seeds works to marvelous effect. The tart, bright lemon perfectly complements the slightly nutty, crunchy seeds that add texture and interest. A squidgy, just soft enough crumb makes these gluten free muffins stand out. I love to make a batch of lemon poppyseed muffins for spring brunches – and they do double duty for afternoon tea. Let’s get to baking!

So Much to Love!

There’s so much to love about this lemon poppy seed muffins recipe. First, you’ll whisk whole grain oat flour with protein-rich almond flour to form a tender muffin, with yogurt to bring added moisture. Lots of lemon makes these springy muffins truly irrestible!

  • Simple ingredients: I love a recipe where I recognize every ingredient in the recipe card. You won’t find anything fancy on the ingredients list, and it’s all easily available at your local grocery store.
  • Gluten free: Just two gluten free flours, including oat flour and almond flour, are the only flours needed to make these into gluten free muffins! The rest of the ingredients are also naturally gluten free. Plus, no gritty, store-bought gluten free flour mix to deal with.
  • Keeps well: Unlike some gluten free recipes, these lemon muffins last for days without drying out! I’ve given you some storage options lower down in this post.
The ingredients for lemon poppyseed muffins are portioned and labelled: eggs, yogurt, poppyseeds, sugar, baking powder, lemon almond flour, oat flour, butter, milk.

Ingredients Needed

There’s nothing complicated on this ingredients list, which includes basics you may have already! Poppy seeds can get expensive – I sometimes buy a larger bottle online for economy’s sake.

  • Oat flour – Gluten-free oat flour is a wonderful choice for baking. See substitution options below if you can’t eat oats.
  • Almond flour – Fine ground almond flour is best here, and it adds wonderful moisture and structure to the muffins.
  • Baking powder – For a little lift.
  • Salt – I always use fine sea salt in my recipes!
  • Butter – Use unsalted butter so that it doesn’t compete with the sweetness of the muffins.
  • Lemon zest
  • Granulated sugar – As noted lower down, if you wish you can decrease the amount of sugar a bit.
  • Eggs – Most recipes are written calling for large eggs unless otherwise specified, so, use large eggs!
  • Yogurt – Use whole-fat or low-fat plain yogurt. Plain is important!
  • Poppy seeds
  • Milk – I like whole milk for richness; 2% milk will also work.
A cup of coffee and a muffin on a white background.

How to Make Gluten Free Lemon Poppy Seed Muffins

You’ll have no issues making these muffins, and I’ve outlined how to do it below! The more detailed instructions are included in the recipe card lower down.

  • Prep: Line a 12-cup muffin tin with liners.
  • Combine dry ingredients: In a medium bowl, whisk the flours, baking powder, poppyseeds, and salt.
  • Cream butter: Rub the lemon zest into the sugar the beat in the butter. Add the yogurt, then the eggs one at a time.
  • Combine: Fold the dry mix into the wet mix, alternating with the milk.
  • Portion out: Divide the batter equally between the muffin cups and rest it while you heat the oven to 375℉. Divide the batter evenly into the muffin tin and rest it while the oven heats.
  • Bake: Place the muffins in the oven and bake for about 25-30 minutes. Cool muffins completely before serving.
A gluten free lemon poppy seed muffin is cut in half on a plate.

Recipe Tips & Substitutions

For the best gluten free lemon poppy seed muffins, try a few of my tips below. I’ve also included some substitution options if you need to make some swaps.

  • Rest the batter. Gluten-free flours benefit from a rest to let them absorb liquids in the batter, which makes for a better structured and tender final product. You can rest the batter in the tin while the oven preheats.
  • Let the muffins cool completely.  The muffins will be quite soft and tender after being baked so it’s important to cool them thoroughly. Let the muffins cool in the pan for 5 minutes, then turn them out on a wire rack to cool for at least another 30 minutes. This will help the crumb to set, making for a sturdier final muffin.
  • Make it less sweet. If you prefer a less sweet muffin, lower the amount of sugar to ⅔ cup rather than 1 cup.
  • Another citrus. Lemon and poppyseeds are a classic combo, and it works well with other citrus too! Try lime or orange zest for the lemon zest for a different flavor.
  • Add fruit. To make these into berry lemon poppyseed muffins, add 2 cups of fresh or frozen blueberries or raspberries.
  • Substitute gluten free flour blend: If you want to use a gluten free flour blend, substitute 2 cups (240 grams) of gluten free all-purpose flour. May I suggest my simple gluten free flour blend?
  • Oat flour substitute: Whole grain, gluten-free sorghum flour is a natural substitute for oat flour as it performs similarly to oat flour. Swap in sorghum flour by weight. Or, substitute brown rice flour by weight for the oat flour.
  • Almond flour substitute: You can make these muffins with all oat flour, or swap another nut flour for the almond flour.
  • Make them refined sugar-free: Easily make this gluten free muffin recipe refined sugar-free by using coconut sugar or honey for the granulated sugar.
  • Go dairy-free: Instead of butter, use melted coconut oil plus your favorite non-dairy milk to make these muffins dairy-free.
Gluten free lemon poppyseed muffins on plates.

Serving Suggestions

Muffins are perfect when served during brunch or you can enjoy them for breakfast. I love a gluten free lemon poppy seed muffin as a mid-morning or afternoon snack, either with a hot cup of coffee or a cup of tea. Sometimes I’ll spread them with a little butter or honey, or even cream cheese, but they are perfectly wonderful served plain, too.

A plate of lemon poppy seed muffins with a halved muffin on a plate in front of it.

Storage Options

Here’s how to store your lemon poppyseed muffins in three different ways:

  • Counter – Keep muffins in an airtight container on the counter for up to 3 days.
  • Fridge – Place muffins in an airtight container for up to 5 days in the refrigerator. You can eat them cold, let them come to room temperature, or gently reheat them in a toaster oven or microwave.
  • Freezer – Put the muffins in a freezer-safe, sealable bag and store them in the freezer for up to 3 months. Defrost in the fridge before serving.

More Easy Gluten Free Muffin Recipes

A lemon poppy seed muffin is cut in half on a plate to show its crumb.

Lemon Poppy Seed Muffins

Nicole Spiridakis
These gluten free lemon poppy seed muffins are sweet and fragrant with lemon and balanced by crunchy poppy seeds scattered throughout. Oat flour and almond flour combine to create a sturdy yet tender crumb that's beautifully gluten free.
5 from 1 vote
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Course Breakfast
Cuisine American
Servings 12 muffins
Calories 221 kcal

Ingredients
  

  • 1 ½ cups oat flour (200 grams)
  • ½ cup almond flour (40 grams)
  • 2 teaspoons baking powder
  • 4 teaspoons poppy seeds
  • ¼ teaspoon fine sea salt
  • ½ cup unsalted butter, at room temperature
  • 1 teaspoon finely grated lemon zest
  • 1 cup granulated sugar
  • 2 large eggs, at room temperature
  • ½ cup plain yogurt
  • ½ cup whole milk

Instructions
 

  • Line 12-cup muffin tin with liners. In a medium bowl, whisk the flours, baking powder, poppyseeds, and salt.
  • In a large bowl, rub the lemon zest into the sugar until it's fragrant. Then, using an electric mixer, cream the butter with the sugar until light and fluffy, about 2 minutes. Scrape down the sides of the bowl and mix in the yogurt, then beat in the eggs one at a time.
  • Using a rubber spatula, fold in the flour in 3 parts, alternating with the milk in 2 parts, until just combined. Take care not to overmix the batter.
  • Preheat the oven to 375℉. Divide the batter evenly into the muffin tin and rest it while the oven heats. Then place the muffins in the oven and bake until a tester comes out clean, about 25-30 minutes. Cool muffins in the pan on a rack, then turn out onto a rack to cool completely.

Nutrition

Calories: 221kcalCarbohydrates: 22gProtein: 3gFat: 13gSaturated Fat: 6gPolyunsaturated Fat: 2gMonounsaturated Fat: 4gTrans Fat: 0.3gCholesterol: 54mgSodium: 129mgPotassium: 85mgFiber: 1gSugar: 12gVitamin A: 296IUVitamin C: 0.01mgCalcium: 92mgIron: 1mg
Did you make this recipe?Let me know in the comments how it went!

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