Gluten Free Lemon Poppy Seed Muffins (Made With Greek Yogurt)

These gluten free lemon poppy seed muffins are tangy, soft, and bakery-style, made with a Greek yogurt batter and bright fresh lemon. Topped with a sweet coconut butter glaze and ready in about 40 minutes.

These started as my grandma’s recipe. Hers used sour cream, and I swapped in plain Greek yogurt for the same moisture with a little protein, and a tang that plays right into all that fresh lemon. I made them a few times, tweaking the ratio until the crumb came out soft instead of dense, and now this is the version I keep.

Gluten free lemon poppy seed muffins are soft, bakery-style muffins made with a gluten-free flour blend, Greek yogurt, and fresh lemon juice and zest, then finished with a sweet glaze. They’re tangy, moist, and naturally gluten-free, with a slightly crisp top and that lemon-and-poppy-seed flavor that tastes like the muffins from the bakery case. The Greek yogurt is the move here, it keeps a gluten-free crumb tender where a lot of GF muffins go dry and crumbly.

Fresh lemon is doing the heavy lifting, so use a real lemon for both the juice and the zest. Bottled juice does not have the same punch, and the zest is where most of that bright flavor lives. If you love a good gluten-free bake, my Healthy Gluten Free Twix Bars and my 3 Ingredient Mini Gluten Free Bagel Bites are worth a look next.

Ingredients You Need

Names and notes here. Exact amounts are in the recipe card below.

For the muffins

• Gluten-free flour with xanthan gum — A 1:1 blend so it swaps cleanly for regular flour. If your blend doesn’t have xanthan, add a little, it’s what holds the crumb together.
• Baking powder and baking soda — Your rise. The baking soda also reacts with the lemon juice for a taller, fluffier top.
• Granulated sugar — Sweetens and helps the edges crisp. A 1:1 sugar replacement works if you prefer.
• Fresh lemon — Juice and zest, from a real lemon. This is the whole flavor, so don’t reach for the bottle.
• Salt — A pinch, to balance the sweet.
• Poppy seeds — The nutty crunch and the classic look.
• Butter — Creamed for a rich, tender crumb. Vegan butter works too.
• Eggs — They bind everything, which matters more in gluten-free baking.
• Plain Greek yogurt — The swap from grandma’s sour cream. Keeps the muffins moist and adds a little protein.

For the glaze

• Coconut butter — My go-to, melted and drizzled. It sets into a soft sweet shell. (I love coconut butter, I put it in coffee, I eat it off the spoon, we don’t need to talk about it.)
• Or a classic lemon glaze of powdered sugar whisked with fresh lemon juice for more tang.

How To Make Gluten Free Lemon Poppy Seed Muffins

1. Prep the muffin tin. Preheat your oven to 350°F. Line a 12-cup muffin tin with liners or grease it well.
2. Mix the dry ingredients. In a large bowl, whisk together the gluten-free flour, baking powder, baking soda, sugar, lemon zest, salt, and poppy seeds.
3. Mix the wet ingredients. In a separate bowl, cream the butter with a mixer until smooth. Add the eggs one at a time, then mix in the Greek yogurt and the juice from one whole lemon.
4. Combine. Add the dry ingredients to the wet and mix until just combined. Don’t overmix, that’s what makes muffins rubbery.
5. Fill the muffin tin. Divide the batter between the 12 liners, filling them right to the brim for tall bakery-style tops.
6. Bake for 18 to 20 minutes, until the tops are set and a toothpick comes out clean.
7. Cool and glaze. Let them cool completely, then glaze with melted coconut butter, or a powdered sugar and lemon glaze, and finish with more poppy seeds and lemon zest.

Tips For Tall, Bakery-Style Muffins

• Fill the muffin liners all the way to the brim. A thick batter scooped high is what gives you those rounded bakery tops instead of flat ones.
• Weigh your gluten-free flour if you can, since even a few extra tablespoons can turn the crumb dry, or spoon-and-level it if you’re using measuring cups.
• Don’t overmix. Stop mixing the second the dry streaks disappear, because overmixing gluten-free batter makes dense, heavy muffins.
• Let them cool fully before you glaze, gluten-free bakes keep setting as they cool and slicing in early leaves a gummy center.
• Substitutions. A gluten-free 1:1 flour is perfect here, no extra ingredients needed. For dairy-free, use vegan Greek yogurt and vegan butter. I haven’t tested these with an egg replacer, since there are three eggs and that’s a lot to sub, so I can’t promise the texture if you go eggless.

How To Store And Freeze

Keep leftover muffins in an airtight container at room temperature for up to 3 days. If you used the coconut butter or glaze, store them in the fridge instead.

They freeze well too, up to 3 months in an airtight container. Defrost on the counter to room temperature, then warm in a 300°F oven or the microwave for a few minutes to bring them back.

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5 from 5 votes

Gluten Free Easy Lemon Poppy Seed Muffin Recipe

These Gluten Free Lemon Poppy Seed Muffins are soft, tangy, and bakery-style, made with Greek yogurt and fresh lemon. Topped with a sweet glaze, ready in 40 min.

Prep Time20 minutes mins

Cook Time20 minutes mins

Total Time40 minutes mins

Course: Breakfast

Cuisine: American

Servings: 12 muffins

Calories: 227kcal

Author: Bailey Campbell

Cook ModePrevent your screen from going to sleep

Ingredients 

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• 1 ¾ cup gluten free flour with xanthan gum
• 1 tsp baking powder
• ½ tsp baking soda
• 1 cup granulated sugar
• 1 lemon for juice and the zest
• Pinch of salt
• 2 tbsp poppy seeds
• ½ cup butter
• 3 eggs
• 1 cup plain greek yogurt

Instructions

• Preheat oven to 350F. Grease and line a 12 cup muffin tin and set aside.
• In a medium size bowl, combine flour, baking powder, baking soda, sugar, lemon zest, salt and poppy seeds.
• In a separate bowl using an electric mixer or stand mixer, cream the butter very well.
• Add in eggs one at a time. Then add greek yogurt and lemon juice from one whole lemon and mix well.
• Add dry ingredients to wet ingredients and mix until just combined. Don't overmix.
• Fill the 12 cup muffin tin and bake for 18-20 minutes.
• Glaze with melted coconut butter (or powdered sugar mixed with more fresh lemon juice), more poppy seeds and lemon zest.

Notes

Substitutions – To make these dairy-free, use vegan Greek yogurt and butter. 

Rounded Muffin Tops – Fill your muffin liners all the way to the brim for big bakery-style muffins.

Storage – Keep muffins in an airtight container at room temperature or glazed muffins in the fridge for up to 3 days.

Freezing – Store in the freezer up to 3 months in an airtight container. Defrost on the counter to room temperature, then warm in a 300°F oven or the microwave for a few minutes to bring them back.

Nutrition

Serving: 1muffin | Calories: 227kcal | Carbohydrates: 31g | Protein: 5g | Fat: 10g | Saturated Fat: 5g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 0.3g | Cholesterol: 62mg | Sodium: 164mg | Potassium: 65mg | Fiber: 2g | Sugar: 18g | Vitamin A: 298IU | Vitamin C: 5mg | Calcium: 82mg | Iron: 1mg

The nutrition information provided is calculated based on industry-standard software and should be used as a general guide only. The information may vary depending on ingredient substitutions, cooking techniques, and individual serving sizes. It is the responsibility of the reader to ensure the accuracy and appropriateness of the nutritional information provided. Always consult a qualified healthcare provider for personalized medical or nutritional advice.

Tried this recipe?Please leave a comment on the blog or share a photo on @basicswithbails

More Gluten Free Recipes To Try

• Superfood Protein Breakfast Cookies (Gluten Free & Vegan)
• Perfect Vegan & Gluten Free Chocolate Chip Cookies
• Gluten Free Vegan Peanut Butter Cookies
• Key Lime Pie Overnight Oats (Gluten Free + High Protein)
• Homemade Dunkaroo Dip (Funfetti Cake Batter Dip)

If you make these, leave a star rating and a comment below. I love hearing how they turned out and whether you went with coconut butter or lemon glaze. And tag @basicswithbails or #basicswithbails if you bake a batch, a tray of these with the glaze still setting is a photo I always want to see.