Lemon Poppy Seed Muffins! Moist and bursting with bright citrus flavor, with a little added crunch from the poppy seeds. A delicious morning treat!

Best Lemon Poppy Seed Muffins Recipe

At this time of year, when the days are short, and the weather is gloomy, I love nothing more than a bright, sunny citrus treat. Seasonal fruit can be scarce in winter, and lemons make you feel so happy and warm!

Some of my favorite lemon recipes include Lemon Cupcakes, Lemon Pound Cake, and Homemade Lemon Curd.

And these perfect lemon poppy seed muffins are a great addition to that collection. They’re easy to make, so moist, and just bursting with tons of bright lemon flavor, with a little bit of added crunch from the poppy seeds.

A great way to treat yourself in the morning! This is one good muffin!

Easy Lemon Poppy Seed Muffins Recipe

Table of Contents

Jump to Recipe

Why this is the best lemon poppy seed muffin recipe

Flavor: Homemade lemon poppy seed muffins burst with zesty lemon flavor. The combination of lemon zest and juice infuses the muffins with a refreshing citrusy tang that’s both sweet and slightly tart.

Texture: The poppy seeds in these muffins add a nice crunch and texture contrast to the otherwise soft, moist muffin.

Customizable: You can tailor homemade lemon poppy seed muffins to your preferences. Adjust the level of lemon flavor, top them in a fun way, or even add extra ingredients like berries or nuts to suit your taste.

Simple: Homemade muffins are really easy to bake, even for a newbie baker!


Flour: All-purpose flour is my go-to, but you can swap it out for any kind of whole-grain option if you like. You may need slightly less if you go that route.

Sugar: Sugar adds sweetness (obvs!) but it also aids in browning and keeps things moist, since it’s hydrophilic (this means it loves water, in other words, it draws moisture in). Regular white sugar is fine, or sub for another type of sweetener if you like. As long as it swaps 1:1 for granulated sugar it should work.

Poppy seeds: Adds a nice crunchy texture to these muffins.

Baking powder: Baking powder is a double-acting leavener, so it starts the muffins rising both when liquid is added to it, as well as when it hits the hot oven.

Salt: Salt carries the flavors and intensifies them. The end result won’t taste salty, but it will make everything so much more flavorful! I like kosher salt best because it doesn’t have any additives that could cause a bitter aftertaste (like iodine). It’s also inexpensive and easy to find in a regular grocery store.

Lemon: The zest and juice of fresh lemon as well as a few drops of lemon extract give these muffins the brightest flavor!

Butter: I like to use unsalted butter because it lets me control the amount of salt in the dish. Different brands of butter can contain different amounts of salt, so this way you get a more consistent result. For a vegan or dairy-free lemon poppy seed muffin recipe, try using coconut oil instead. Melt the butter and allow it to cool slightly before adding it to the batter.

Greek yogurt: Creates an extra thick batter that yields light and tender muffins. Sour cream can be substituted.

Milk: Whatever kind you usually keep on hand. Even a plant-based product will work!

Eggs: Use large chicken eggs or a 1:1 plant-based substitute, preferably at room temperature (although I don’t find this to be critical).

Variations and substitutions

Muffin recipes are generally pretty forgiving and will still work well even if you need to sub out certain ingredients. Here’s info on some of the most common substitutions I get asked about:

Gluten-free lemon poppy seed muffins: To make gluten-free lemon poppy seed muffins, substitute the all-purpose flour for a gluten-free flour blend. Look for one that subs 1:1 for regular flour.

Here are a few good options:

Lemon muffins without yogurt: Greek yogurt makes for a slightly healthier muffin, but sour cream can be substituted if you don’t have it. This will provide a really rich flavor and a moist texture.

How to make lemon poppy seed muffins

These sunshine-y treats come together in just 5 simple steps.

Step 1: Combine the dry ingredients

Place the flour, sugar, poppy seeds, baking powder, salt, and lemon zest in a large bowl and whisk to combine. 

Stirring dry ingredients for lemon poppy seed muffins together with a whisk.

Step 2: Combine the liquid ingredients

Melt the butter in a large liquid measuring cup and whisk in the Greek yogurt, milk, eggs, lemon juice, and lemon extract. 

Whisking liquid ingredients for lemon poppy seed muffins together in a liquid measuring cup.

Step 3: Add liquid to dry

Pour the liquid ingredients into the dry, and fold until barely combined (the batter will be very thick). 

Stiff lemon poppy seed muffin batter in a mixing bowl.

Step 4: Bake

Divide the batter equally between all 12 muffin cups.  

Unbaked lemon poppy seed muffins in  a standard-sized muffin tin.

Blast the muffins first with high heat to get a tall rise, then turn the oven temp down and continue to bake them through, until a toothpick inserted in the thickest part of a muffin comes out clean or with a few moist crumbs.

Step 5: Glaze

Drizzle generously with a tangy lemon glaze, made by stirring powdered sugar and lemon juice together.

Drizzling a lemon poppy seed muffin with lemon glaze.

Expert tips for the perfect poppy seed muffin

  • Allow ingredients like eggs, butter, and milk to come to room temperature before using them. This ensures even mixing and better incorporation.
  • Use fresh lemons. Their flavor can’t be beat!
  • Don’t overmix. Once your batter is barely combined, scoop it into your muffin pan.
  • Fill each muffin tin all the way up.
  • You will need about 3/4 of a cup of batter for each muffin. It looks like a lot, but that is how you get those sky-high, puffy muffin tops!
  • Allow muffins to cool briefly in the tin before transferring them to a wire rack. Cooling on a rack prevents them from becoming soggy due to trapped steam.
  • Make sure your baking powder, baking soda, and other leavening agents are fresh. Check the expiration date!
Lemon Poppy Seed Muffins From Scratch


Is the batter supposed to be thick?

This muffin batter is meant to be very thick!

At first, you might think it’s too dry to come together, but it does! If you don’t believe me, check out the video in the recipe card below.

As you can see, if you keep folding, it eventually comes together into a thick, sticky batter. A thicker, stiffer muffin batter makes for a tall, puffy, bakery-style muffin. No flat-topped muffins here!

Even though the dough is stiff, the muffins will still be very light, fluffy, and moist. It’s like magic!

What is the best glaze to use to top lemon poppy seed muffins?

These muffins are fantastic as-is, but they’re even better drizzled with a tangy, citrus-y lemon glaze. It’s really easy to make!

Just stir powdered sugar and lemon juice together until you get a nice, drippy consistency. Then squiggle it over the muffins and allow it to set for about 20 minutes.

What other ways can you top these muffins?

If you don’t feel like making a glaze, clear sanding sugar is another great option. I use this coarse, sparkly sugar a lot for garnishing muffins. It gives extra sweetness and a little bit of crunch.

Or try my favorite basic streusel recipe! This crumb topping would be fantastic made with white sugar and lemon zest.

Moist Lemon Poppy Seed Muffins

How to serve

Plain and simple: Serve the muffins as is, at room temperature or slightly warmed. They are delicious on their own and perfect for breakfast or an afternoon snack.

Butter or cream cheese spread: Slice the muffin in half and spread a thin layer of butter or cream cheese on each half. This adds a richness and creaminess that pairs well with the lemony tang and poppy seed crunch.

Fresh berries: Serve with a side of fresh berries like strawberries, blueberries, or raspberries. The tartness of the berries complements the muffins’ sweetness.

Lemon curd: Spoon some lemon curd onto your muffin or serve it on the side. Lemon curd is a tangy, sweet spread that pairs beautifully with lemon poppy seed flavors.

How to store

Room temperature: Once baked, these muffins can sit out at room temperature for 1-2 days. I actually like to keep them in the muffin pan, and just cover them loosely with plastic wrap. I find that if they are tightly covered or kept in an airtight container, they tend to become a little soggy. And if they are drizzled with glaze, that’s not really a good thing because the glaze will weep. A loose covering is best, to allow a little airflow but still keep things somewhat moist.

Freeze: Place muffins in a zip-top bag. They will keep for about 2 months in the freezer. Pop them in the microwave for 15 to 20 seconds to thaw and re-warm.

How to Make Homemade Lemon Poppy Seed Muffins

Mix up a batch of these sunny lemon poppy seed muffins! They’re so quick and easy to make, and they make such a special treat for breakfast, brunch, or snack.

A few more of my best quick bread recipes

This post contains affiliate sales links.

Best Lemon Poppy Seed Muffins Recipe
4.44 stars (16 ratings)

Lemon Poppy Seed Muffins

Servings: 12 muffins
Prep Time: 15 minutes
Cook Time: 20 minutes
Total Time: 35 minutes
Lemon Poppy Seed Muffins! Moist and bursting with bright citrus flavor, with a little added crunch from the poppy seeds. A delicious morning treat! 


For the lemon poppy seed muffins:

  • 2 1/2 cups (375 g) all-purpose flour
  • 1 cup (200 g) sugar
  • 2 tablespoons poppy seeds
  • 1 tablespoon (1 tablespoon ) baking powder
  • 1/4 teaspoon (0.25 teaspoon) kosher salt
  • 1 tablespoon (1 tablespoon ) lemon zest , (zest of 1 lemon)
  • 1/2 cup (113.5 g) unsalted butter, , melted
  • 1 cup (200 g) plain Greek yogurt*
  • 1/4 cup (61 ml) milk
  • 2 (2) eggs, , large
  • 3 tablespoons lemon juice, (juice of 1 lemon)
  • 1 teaspoon lemon extract

For the lemon glaze:

  • 1 1/2 cups (180 g) powdered sugar
  • 3 tablespoons lemon juice , (juice of 1 lemon)


To make the lemon poppy seed muffins:

  • Preheat the oven to 425 degrees F, and line a muffin pan with papers. 
  • Place the flour, sugar, poppy seeds, baking powder, salt, and lemon zest in a large mixing bowl, and whisk to combine. 
  • Melt the butter in a large liquid measuring cup, and whisk together with the Greek yogurt, milk, eggs, lemon juice, and lemon extract. 
  • Pour the liquid ingredients into the dry, and fold together until just barely combined (batter will be very thick). 
  • Divide the batter equally between all 12 wells of the muffin pan. 
  • Bake the muffins for 5 minutes at 425 degrees F, then turn the oven temperature down to 350 degrees F and continue to bake for 14 to 18 minutes, or until a toothpick inserted in the thickest part of a muffin comes out clean or with a few moist crumbs.
  • Drizzle with lemon glaze and serve. 

To make the lemon glaze:

  • Place the powdered sugar in a medium bowl, and stir in the lemon juice, a little at a time, until the desired consistency is achieved. 


*Sour cream may be substituted.
A few more of my favorite muffin recipes:
Calories: 338kcal, Carbohydrates: 57g, Protein: 6g, Fat: 9g, Saturated Fat: 5g, Cholesterol: 48mg, Sodium: 70mg, Potassium: 193mg, Fiber: 1g, Sugar: 32g, Vitamin A: 285IU, Vitamin C: 3.5mg, Calcium: 100mg, Iron: 1.8mg
Cuisine: American
Course: Breakfast, Brunch, Snack
Tried this recipe?Mention @bakingamoment on Instagram or tag #bakingamoment.


  • Allie

    Allie is the creator and owner of Baking a Moment. She has been developing, photographing, videographing, and writing and sharing recipes here since 2012.