Lemon Poppy Seed Muffins are a favorite breakfast here at my house. They're the perfect combination of sweet and tangy - the zippy flavor of citrus in the morning is sure to wake you up. Plus, they're easy to grab and take on-the-go.
These muffins have a light yet moist lemon-flavored crumb with poppy seeds perfectly dispersed throughout. Then, they're topped with a mouth-watering lemon cream cheese glaze. This combo is perfection.
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Looking for more gluten free breakfast baked goods?
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- Chocolate Banana Bread - Gluten Free Banana Bread Recipe
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What makes Gluten Free Lemon Poppy Seed Muffins so good?
- High quality gluten-free all purpose flour containing xanthan gum. I always recommend to avoid using GF flour blends that contain ingredients such as garbanzo bean/chickpea flour, pea protein, lentil flour, etc. in desserts because it can leave a strange aftertaste. In this recipe, I used Bob's Red Mill Gluten Free 1:1 Baking Flour (the blue bag).
- Freshly-squeezed lemon juice. Since these muffins are all about glorious lemon flavor, it's important to use fresh lemons and not the stuff in a bottle. I don't recommend lemon extract because it's much more concentrated than lemon juice.
- Lemon zest.
- Pure vanilla extract. We can't have a baked good without it around these parts.
- Greek yogurt. This healthy source of added fat keeps the muffins moist and adds a little tang.
- Granulated sugar.
- Vegetable oil or oil of choice. I love using oil in my baked goods because it keeps them moist even at cooler temperatures like when refrigerated, unlike butter which hardens.
- Organic poppy seeds. I buy mine from Thrive Market (Get 40% off your first order + sometimes a free gift.).
- Homemade lemon cream cheese icing.

How to Make Gluten Free Lemon Poppy Seed Muffins:
- Preheat oven to 400 F. Prepare a muffin tray by greasing it with a little bit of butter or placing down cupcake liners, or using a silicone muffin tray.
- In a medium-sized mixing bowl, whisk together GF flour, baking soda, and salt. Set aside.
- In a large-sized mixing bowl, whisk together oil, sugar, yogurt, eggs, vanilla extract, lemon juice, and lemon zest. Mixture should be very smooth.
- Add the dry ingredients to the wet and stir until just combined. Tip: Do not over-mix.
- Stir in poppy seeds.

- Spoon batter into the muffin tray cups ⅔ of the way full.
- Bake 10-12 minutes, or until lightly browned and a toothpick inserted in the center comes out clean. Remove from oven. Allow to cool in tray for 5 minutes before removing to a wire cooling rack until completely cool.


- Meanwhile, set the butter and cream cheese out for the icing to become room temperature.


- For the Lemon Cream Cheese Icing: In a small mixing bowl, cream butter and cream cheese together until smooth. I use an electric handheld mixer. Then, add in powdered sugar and lemon juice. Beat until smooth.

- Once the muffins are completely cool, drizzle icing over top with a spoon.
- Enjoy. Store all leftovers in an airtight container in the refrigerator and eat within 3 days.


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Gluten Free Lemon Poppy Seed Muffins
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Equipment
Ingredients
For the Lemon Poppy Seed Muffins:
- 1 ⅓ cups high-quality GF all-purpose flour containing xanthan gum I used Bob's Red Mill GF 1:1 Baking Flour (the blue bag)
- ¾ cup granulated sugar
- ½ teaspoon baking soda
- ½ teaspoon salt
- ¾ cup Greek yogurt (plain or vanilla)
- 2 large eggs
- 3 tablespoon vegetable oil
- 1 tablespoon freshly-squeezed lemon juice
- 1 teaspoon pure vanilla extract
- zest of one large lemon
- 1 tablespoon poppy seeds
For the Lemon Cream Cheese Icing:
- 1 tablespoon butter room temperature
- 1 tablespoon cream cheese room temperature
- ½ cup powdered sugar
- 4 teaspoon freshly-squeezed lemon juice
Instructions
- Preheat oven to 400 F. Prepare a muffin tray by greasing it with a little bit of butter or placing down cupcake liners, or using a silicone muffin tray.
- In a medium-sized mixing bowl, whisk together flour, baking soda, and salt. Set aside.
- In a large-sized mixing bowl, whisk together oil, sugar, yogurt, eggs, vanilla extract, lemon juice, and lemon zest. Mixture should be very smooth.
- Add the dry ingredients to the wet and stir until just combined. Tip: Do not over-mix.
- Stir in poppy seeds.
- Spoon batter into the muffin tray cups ⅔ of the way full.
- Bake 10-12 minutes, or until lightly browned and a toothpick inserted in the center comes out clean. Remove from oven. Allow to cool in tray for 5 minutes before removing to a wire cooling rack until completely cool.
- Meanwhile, set the butter and cream cheese out for the icing to become room temperature.
For the Lemon Cream Cheese Icing:
- In a small mixing bowl, cream butter and cream cheese together until smooth. I use an electric handheld mixer. Then, add in powdered sugar and lemon juice. Beat until smooth.
- Once the muffins are completely cool, drizzle icing over top with a spoon.
- Enjoy. Store all leftovers in an airtight container in the refrigerator and eat within 3 days.
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