This is the best recipe for Lemon Poppy Seed Muffins if you’re a fan of big, fluffy bakery-style muffins with those beautiful domes. Full of real lemon flavor and studded with poppy seeds, this is one treat you’re not going to want to miss!

frontal view of glazed lemon poppy seed muffins in front of milk bottle

Muffins are such a great baked good to make. They’re quick to bake and conveniently portioned out. And with my tips and techniques, you can achieve the most beautiful domes!

I love the tangy lemon flavor paired with the poppy seeds – almost like a Lemon Loaf Cake, but breakfast-friendly ? You don’t have to add the glaze, instead spread them with butter or cream cheese if you want to stick to a breakfast-theme… but I do think the lemon glaze makes them an extra special treat!

Ingredients you’ll need

Here is a visual overview of the ingredients in the recipe. Scroll down to the printable recipe card at the bottom of this post for quantities!

ingredients for lemon poppy seed muffins with text labels — *Ingredients for Lemon Poppy Seed Muffins: Flour, sugar, poppy seeds, baking powder, baking soda, salt (missing in photo!), Greek yogurt, lemon juice, lemon zest, melted butter, eggs and icing sugar.*

Ingredient notes

Flour: I use all-purpose flour here. If you want to add some whole grains, feel free to swap half of the all-purpose flour for whole wheat. You may need to add 1-2 tablespoons of milk to the batter if it’s too thick. I cannot advise on using an alternative flour like almond, because the behavior in baking of these types of flour are very different from wheat.
Butter: A neutral vegetable oil is fine to use in place of the melted butter.
Lemon juice: Fresh is best, but bottled works in a pinch.
Greek yogurt: I use plain full-fat Greek yogurt. You can use low fat, but it must be Greek yogurt, not regular yogurt. A thick sour cream can be used in place of the Greek yogurt.
Baking powder and soda: I highly recommend using both in this recipe, for best results. If you only want to use one type, it should be the baking powder.

Recipe variations

Coconut: Try reducing the flour by ¼ cup, and add ½ cup shredded toasted coconut to the dry ingredients. A great twist for spring and summer!
Lemon curd: Use spoonfuls of lemon curd in the muffin centres for a tasty surprise. Spoon ⅔ of the batter into the prepared muffin cups. Add a heaping teaspoon of lemon curd into the middle of each muffin, then divide the remaining batter on top of the muffin cups. Bake as directed.
Raspberries: Fold 1 cup of fresh or frozen raspberries (do not thaw if frozen) into the batter.

How to make Lemon Poppy Seed Muffins

1. Dry ingredients: Start by combining the dry ingredients in a medium mixing bowl. I use a whisk to break up the flour and evenly distribute the poppy seeds, baking powder, soda and salt for better rising and better taste.

2. Wet ingredients: Whisk together the wet ingredients in a separate bowl. I like to use a large measuring cup here, for easy pouring in the next step.

overhead view of dry ingredients for lemon poppy seed muffins in glass bowl with whisk — combine dry ingredients

overhead view of wet ingredients for lemon poppy seed muffins in glass measuring cup with whisk — combine dry ingredients

3. Combine: Add the wet to the dry ingredients. Use a wooden spoon or rubber spatula (NOT the whisk!) to combine them into a thick batter. A few lumps are fine, but make sure no more dry flour is visible. Do not overmix – you want to carefully fold, not vigorously stir.

4. Scoop: Scoop the muffin batter into lined muffin cups. I use an ice cream scoop for this – it’s SO easy and absolutely mess free! Even young kids can do this without getting batter all over the kitchen.

muffin pan with lined cups filled with muffin batter — fill muffin cups

overhead view of muffin pan on cooling rack with baked muffins in cups — fill muffin cups

5. Bake: I bake muffins in a special way, to really get those nice and big domes on them

I preheat the oven to 425°F (yes, really).

Right before I out the muffins in the oven, I reduce the temperature to 400°F. I bake the muffins at 400°F for 5 minutes.

Then WITHOUT OPENING THE OVEN, I reduce the oven temperature to 360°F and finish baking for 15-18 minutes, until a toothpick entered into the middle of a muffin comes out with no more wet batter sticking to it.

6. Cool and glaze: Let the muffins cool in the pan for 5 minutes, before removing them to a cooling rack to cool completely. If you want to use the glaze, combine the icing sugar with just enough lemon juice to make a smooth, thick glaze. Drizzle over the cooled muffins. I garnished with small lemon wedges and poppy seeds.

overhead view of several glazed lemon poppy seed muffins on marble and ceramic surface

Recipe notes

Muffin batter: This batter is on the thick side, but it shouldn’t be overly gloopy. If you think you accidentally added too much flour, you can thin out the batter with 1-2 tablespoons of milk.

Flour measuring: Measuring flour with measuring cups can be quite tricky to get right. You shouldn’t scoop the flour with the cup, instead you need to spoon it into the cup to make sure it’s fluffy – then level it off with a knife. I wrote a post about the “spoon and level” method, which yields the most accurate amount of flour in baking recipes. If you’re unsure about how to measure out your flour, I highly recommend reading it!

Can the batter be made ahead and baked later? I frequently get this question, but I do not recommend doing this. The baking powder is partly activated when they come in touch with liquids and especially with acids (lemon juice!). You’ll want to get the batter into the oven as soon as possible after making it to get the best rise. Otherwise, your muffins may turn out flat.

Recipes for flatter baked goods (like pancake recipes that only rely on baking soda) may turn out better when the batter is left to rest for 15-30 minutes, but this is not the case here, so I recommend baking right away.

Quick tips

Don’t use a whisk when combining the wet and dry ingredients – use a rubber spatula or a wooden spoon to avoid overmixing.
An ice cream or cookie scoop makes it virtually mess-free to transfer the batter into the muffin cups.
My favorite muffin liners are from If You Care – the only ones I’ve ever found that never stick to the muffins!
For the perfect domed muffins, stick to the oven temperature instructions in the recipe. The initial boost of heat quickly activates the baking powder and causes the muffins to rise very nicely.

overhead view of lemon poppy seed muffin with bite taken out

Storage

Make ahead: Store the muffins in an airtight container for 2 or 3 days on the counter, or for 3-4 days in the fridge. If using the glaze, it will soften in the container but still be perfectly delicious.

Freezer: Cool the muffins completely before freezing. Do not glaze. If using a freezer container, make sure the muffins don’t touch. If using freezer bags, you may want to flash-freeze the muffins on a baking sheet, without touching, for an hour before transferring them to bags. This way, you can remove one at a time.

Label the freezer bag or container with the name and use by date, then freeze for up to 2 months.

To defrost, remove from the bag/container and place on a cooling rack on the counter for a few hours, until completely defrosted. The muffins can be warmed in the microwave, or glazed after thawing.

PS If you try this recipe, please leave a review in the comment section and add a star rating in the recipe card – I appreciate your feedback! Follow along on Pinterest, Facebook or Instagram.

Printable recipe

Recipe first published on 04/28/2017. Updated with new photos, new text and a new and improved recipe on 03/16/2023.

Bakery-Style Lemon Poppy Seed Muffins