This post may contain affiliate links.
Allow me to introduce you to the Bakery-Style muffin of your dreams. Or at least, it’s definitely mine. Perfect for Mother’s day, these jumbo muffins will look like they rolled straight out the door of your local bakery and onto your brunch table. Lots of lemon, less sugar than your usual muffin and did I mention they’re gluten free? Make some ahead of time and freeze, or serve them fresh. Melt in your mouth softness with just the right amount of zing.

😍 Why You’ll Love These Lemon Poppy Seed Muffins
Imagine biting into a muffin that transports you straight to your favorite local bakery, all from the comfort of your own home. These lemon poppy seed muffins are a celebration of bright citrus flavor and delicate texture, with just the right amount of sweetness to let the lemon shine. Each bite offers a refreshing zing, balanced by the subtle crunch of poppy seeds and the soft, melt-in-your-mouth crumb that makes bakery-style muffins so irresistible.
What makes these even better is how approachable they are. They’re naturally gluten-free, so everyone can enjoy them, and they’re easy to make ahead of time. Bake a batch, freeze what you don’t need, and you’ll have sunshine on standby whenever the craving hits.
🗒️ Ingredients
Eggs: The secret to a light, fluffy crumb—room temperature makes all the difference.
Sugar: Just enough to balance the lemon’s zing without overpowering it.
Vanilla: A hint of warmth that rounds out the bright citrus flavors.
Oil: Keeps the muffins perfectly moist without weighing them down.
Yogurt: Adds tenderness and a slight tang for bakery-style softness.
Lemon Zest & Juice: The star of the show, bringing fresh, vibrant flavor to every bite.
Flours: A gluten-free blend that bakes up light and tender (or swap for what you have).
Baking Powder & Baking Soda: The duo that gives these muffins their perfect rise.
Salt: Just a pinch to make every other flavor shine.
Poppy Seeds: For a subtle crunch and classic finish.

👩🍳 How to Make My Lemon Poppy Seed Muffins
🔥 Start by preheating your oven to 350°F and spraying a jumbo muffin tin with nonstick baking spray. This ensures your muffins release easily once baked.
🥚 In a large bowl, whisk together the eggs and sugar until light and slightly frothy. Stir in the vanilla, oil, yogurt, lemon zest, and lemon juice until smooth and well combined.
🥣 In a separate bowl, whisk together the flours, baking powder, baking soda, salt, and poppy seeds. Gradually fold the dry ingredients into the wet mixture, using a rubber spatula to combine. Be careful not to overmix—just stir until no streaks of flour remain.
🥄 Divide the batter evenly between the prepared muffin cups, filling them almost to the top. Bake for about 25 minutes, or until the tops are golden and a toothpick inserted into the center comes out clean.
💨 Let the muffins cool in the pan for 10 minutes before transferring them to a wire rack to cool completely. Serve them fresh or freeze for later – they’re delicious either way!
🥳 Enjoy!
🎩 Tips and Tricks
- Room temperature eggs aren’t just a suggestion – they’re the key to achieving that bakery-style rise. Forgot to take them out? Just pop them in a bowl of warm water for five minutes before you start.
- Once you combine the wet and dry ingredients, stir until just combined. Overmixing can lead to dense muffins instead of the soft, airy crumb you’re aiming for.
- If you want that classic domed top, don’t be shy when filling your muffin tin. This recipe is designed to rise beautifully without spilling over.
- Ovens can vary, so start checking for doneness around the 22-minute mark. A toothpick should come out clean, and the tops should spring back when lightly pressed.

🌟 Variations
🍊 Orange Cardamom: Swap the lemon zest and juice for orange, and add a teaspoon of ground cardamom for a warm, aromatic twist.
🍯 Grapefruit Honey: Replace lemon with grapefruit and use honey instead of sugar. The slight bitterness of grapefruit pairs beautifully with the natural sweetness of honey.
🍋🟩 Lime Coconut: Go tropical by substituting lime for the lemon and using coconut yogurt. A sprinkle of shredded coconut on top before baking adds a little texture and flair.
💜 Meyer Lemon Lavender: If you can find Meyer lemons, they’ll add a sweeter, floral note. Stir in a teaspoon of culinary lavender for an elegant touch.
🫐 Lemon Blueberry: Fold in a handful of fresh or frozen blueberries with the dry ingredients. The juicy berries add bursts of sweetness that pair perfectly with the bright lemon.
🤲 Substitutions
- Flour: Swap the gluten-free blend for regular all-purpose flour if you don’t need them to be gluten-free. It works cup for cup.
- Yogurt: For dairy-free, use coconut or almond yogurt. Just make sure it’s unsweetened to keep the balance right.
- Oil: Sunflower, safflower, vegetable, or canola oil all work. Even light olive oil can add a subtle richness.
- Sweetener: To go refined sugar-free, substitute honey or maple syrup. The flavor will be slightly deeper, and the crumb a little more moist.
- Eggs: Need an egg-free option? Use flax eggs (1 tablespoon flaxseed meal + 3 tablespoons water per egg). The texture will be slightly denser but still delicious.
- Citrus: Lemon is classic, but you can easily use orange, grapefruit, or lime. Each one brings its own unique flavor twist.
- Poppy Seeds: No poppy seeds? Chia seeds make a great substitute and add a little extra crunch.

📓 Best served with
- Coffee or tea
- Whipped butter
- Greek yogurt and berries
👝 How to Store Your Lemon Poppy Seed Muffins
Store them in an airtight container at room temperature for up to three days, making sure they’re completely cool before sealing to avoid condensation. If you’d like to extend their shelf life, refrigerate them for up to a week, though the crumb might firm up slightly. For longer storage, freeze the muffins in a single layer on a baking sheet, then transfer them to a freezer-safe bag or container—they’ll keep beautifully for up to three months.
🧠 Common Questions
Absolutely! Just swap the yogurt for a dairy-free alternative like coconut or almond yogurt. Make sure it’s unsweetened to keep the balance of flavors just right.
Not at all. If you’re not avoiding gluten, regular all-purpose flour works perfectly in this recipe, cup for cup.
Yes! While lemon is classic, orange, grapefruit, or even lime all work beautifully. Each brings its own unique flavor profile to the muffins.
The tops should be golden and spring back when lightly pressed. You can also insert a toothpick into the center—if it comes out clean, they’re ready.
Of course! This recipe makes 12 regular-sized muffins. Just reduce the baking time by about five minutes and start checking for doneness around the 20-minute mark.
It’s best to bake the muffins right after mixing the batter. However, you can bake them ahead and freeze them—just reheat when you’re ready to enjoy.

Bakery-Style Lemon Poppy Seed Muffins
Equipment
- 1 Jumbo Muffin Tin
- 1 Large Bowl
- 1 Medium Bowl
- 1 Whisk
- 1 Spatula
Ingredients
- 1 3/4 cup GF Flour Blend
- 1 tsp Baking Powder
- 1/2 tsp Baking Soda
- 2 tbsp Poppy Seeds
- 1/2 tsp Kosher Sea Salt
- 3/4 cup Raw Cane Sugar
- 2 tbsp Lemon Zest
- 1/3 cup Lemon juice
- 1 cup Greek Yogurt, I like 4%
- 1/2 cup Sunflower Oil
- 3 Large Eggs, Room Temperature
- 1/2 tsp Vanilla Extract
Instructions
- Preheat the oven to 350 degrees F.
- Spray a 6-cup jumbo muffin tin with nonstick baking spray.
- In a large bowl, whisk together the eggs and sugar for 30 seconds by hand. Add the vanilla, oil, yogurt, zest and juice from both lemons, and whisk to combine.
- In a separate medium sized bowl, whisk together the flours, seeds, baking powder, baking soda, and salt.
- Add the dry ingredients to the wet ingredients and start with a rubber spatula to combine, then whisk until just combined and there are no traces of flour.
- Transfer the batter equally to the prepared muffin tins and bake until just cooked through, about 25 minutes.
- Cool in the pan for 10 minutes, then remove to a baking rack to finish cooling completely. Serve or freeze.
- Enjoy!
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
I would like to make 12 regular sized muffins. Could you please provide instructions for the modification. Also, given that they are GF, do you recommend refrigerating the muffins for 20 minutes prior to baking and/or resting on the counter at room temperature for 10-20 minutes ? PS I loved your orange poppyseed GF version. Thank you in advance.
Hi there! This recipe makes 6 jumbo muffins, so would make roughly 12 regular sized muffins. The only modification here would be your baking time – I’d suggest checking them with a cake tester around the 12-15 minute mark. When the cake tester comes out clean, they are ready to be removed from the oven! I don’t specifically recommend refrigerating the muffins here – and with a good GF flour blend, you shouldn’t need to. I recommend Bob’s Red Mill 1:1 GF Flour
Absolutely delicious. I used the glaze from your lemon loaf recipe to give them a little added punch of lemon.
That sounds delicious, Tracey!
Enjoy,
Kat.
Will white sugar work instead of the raw cane sugar?
Thanks for sharing your recipes and expertise!
Absolutely, Tracey! White granulated sugar will work fine.
Kat.
Hi! My husband loves almond poppyseed muffins…what would you do to switch that up here? Almond milk instead of lemon juice, no zest and add almond extract? Thoughts?
Thanks!
That sounds like the start of a beautiful Almond Poppyseed muffin to me, Wendi! It may take a bit of tweaking depending on how prominent he likes the almond flavor, but I think you’re on the right track.
Let me know how your experimentation goes!
Kat.
These muffins are delicious!! So lemony, perfect for spring and summer breakfast!!!
Yvonne,
I’m so glad you love them! They’re a brunch staple in my books.
Enjoy!
Kat.
Your recipe does not call for cardamon or ginger, yet in the mixing instructions they are listed. However, no poppyseeds are listed in the mixing directions. getting ready to make these and I will be leaving out the cardamon and ginger and hope that everything else in the recipe is correct.
Hi Donna,
Are you looking at the recipe here on the website? There was a mixup with a site update very briefly, but it’s been fixed now for a few days.
Kat