Gluten Free Lemon Poppyseed Muffins Recipe

Bright, zesty, and naturally gluten-free, these lemon poppyseed muffins are a delightful treat for breakfast, a snack, or dessert.

Made with almond flour and bursting with fresh lemon flavor, these muffins are moist, tender, and topped with a light glaze for a touch of sweetness.

Serve them with your morning coffee, as a mid-afternoon pick-me-up, or even as a light dessert.

Close-up of freshly baked gluten-free lemon poppyseed muffins on a wooden board, garnished with lemon slices

Gluten Free Lemon Poppyseed Muffins

Made with almond flour and bursting with fresh lemon flavor, they’re moist, tender, and topped with a light glaze for a touch of sweetness. Whether paired with your morning coffee, enjoyed as a midday snack, or served as a light dessert, these muffins are sure to impress!
Prep Time 15 minutes
Cook Time 20 minutes
Course Breakfast, Dessert, Snack
Cuisine American
Servings 12 muffins
Calories 210 kcal

Equipment

  • Muffin tin 12-count
  • Muffin liners or parchment paper
  • Large mixing bowl
  • Medium mixing bowl
  • Whisk
  • Spatula
  • Zester or microplane
  • Measuring cups and spoons
  • Cooling rack

Ingredients
  

Muffins

  • 2 cups almond flour
  • 1/4 cup  coconut flour
  • 2 tbsp poppy seeds
  • 1 tsp baking soda
  • 1/4 tsp salt
  • 3 large eggs
  • 1/3  cup  maple syrup or honey
  • 1/4 cup  coconut oil melted
  • 1/4  cup  unsweetened almond milk or milk of choice
  • 1 tsp vanilla extract
  • 2 tbsp fresh lemon juice
  • 2 Zest of lemons

Optional Lemon Glaze

  • 1/2 cup  powdered sugar or a sugar-free substitute
  • 1-2 tbsp fresh lemon juice

Instructions
 

For the Muffins:

  • Preheat the oven: Set your oven to 350°F (175°C). Line a 12-count muffin tin with muffin liners or grease the tin lightly with oil.
    Mix dry ingredients: In a large mixing bowl, whisk together almond flour, coconut flour, poppy seeds, baking soda, and salt until well combined.
    A bowl of almond flour surrounded by lemons, poppy seeds, and salt on a marble surface with a wooden spoon
  • Combine wet ingredients: In a medium bowl, whisk the eggs, maple syrup, melted coconut oil, almond milk, vanilla extract, lemon juice, and lemon zest until smooth.
    Incorporate wet and dry: Gradually pour the wet ingredients into the dry ingredients, stirring gently with a spatula until no lumps remain. Do not overmix.
    A bowl of mixed wet ingredients topped with lemon zest and oats, surrounded by lemon halves on a marble countertop
  • Fill muffin tin: Divide the batter evenly among the muffin cups, filling each about 3/4 full.
    A muffin tin lined with white paper cups, each filled with lemon poppyseed batter, on a marble countertop
  • Bake: Place the tin in the preheated oven and bake for 18–20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
    Cool: Let the muffins cool in the tin for 5 minutes, then transfer to a cooling rack to cool completely.
    Close-up of golden lemon poppyseed muffins topped with poppy seeds on a cooling rack

For the Optional Lemon Glaze:

  • In a small bowl, mix the powdered sugar with 1 tablespoon of lemon juice. Add more lemon juice, a little at a time, until you reach your desired consistency.
    Once the muffins are fully cooled, drizzle the glaze over the tops using a spoon or piping bag. Allow the glaze to set before serving.
    Close-up of gluten-free lemon poppyseed muffins drizzled with lemon glaze, garnished with lemon slices

Video

Notes

Cooking Tips

  • For extra moisture: Add 2 tablespoons of plain Greek yogurt or sour cream to the batter.
  • Substitute sweeteners: If you don’t have maple syrup, honey or agave nectar works well.
  • Intensify the lemon flavor: Add a drop of lemon extract to the wet ingredients if you love a stronger lemon taste.
  • Storage: Store these muffins in an airtight container at room temperature for up to 3 days, or in the fridge for up to a week. Freeze for longer storage and defrost as needed.
Keyword Dairy-free, Gluten-free, Healthy Breakfast

Are there any Alternatives?

If you don’t have all the ingredients on hand or need to make substitutions for Lemon Poppyseed Muffins, this recipe is flexible and can accommodate various alternatives.

For the flour base, almond flour is the star ingredient, but if you prefer, you can substitute it with a 1:1 gluten-free all-purpose flour blend. Keep in mind that the texture will be slightly different, less tender and moist, but still delicious.

Coconut flour plays an important role in absorbing moisture, so if you don’t have it, you can replace it with an additional 1/4 cup of almond flour. However, adjust the wet ingredients slightly, as coconut flour requires more liquid.

For the sweetener, maple syrup can be swapped with honey or agave nectar for a similar level of sweetness and moisture. If you’d like a sugar-free option, try using a liquid sugar substitute like monk fruit syrup. The coconut oil in the recipe can be replaced with melted butter or even olive oil for a slightly different flavor profile.

Almond milk works well as a liquid base, but regular dairy milk, oat milk, or even coconut milk can be used as alternatives. Lastly, for those avoiding poppy seeds or wanting variety, you can replace them with chia seeds for a similar texture or omit them entirely for plain lemon muffins.

Close-up of gluten-free lemon poppyseed muffins garnished with fresh lemon slices and poppy seeds
Poppy seeds are not just decorative—they add a nutty flavor and are a source of fiber, calcium, and magnesium

The Bottom Line

Gluten-free baking doesn’t have to be limiting, and these Lemon Poppyseed Muffins are a testament to that!

With their bright lemony flavor, moist texture, and adaptability to various alternative ingredients, this recipe is as versatile as it is delicious.

The combination of almond flour and coconut flour ensures a gluten-free treat that’s full of flavor and nutrition, while the optional glaze adds a touch of sweetness that’s hard to resist.

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