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These Lemon Poppy Seed Muffins are sure to put a spring in your step. Literally—these muffins are so springy, both in the seasonal sense, and in the moist sense! True lemon flavor bursts in each happy bite along with the subtle crunch of the poppy seeds, with a sweet lemon glaze as a little peppy bonus.

the best lemon poppy seed muffin with a glaze

Baking with fresh lemons, like this Lemon Tart or these quintessential Lemon Bars, makes me think of sunshine, and sunny days are happy ones where I live. 

This lemon poppy seed muffin recipe is adapted from the Lemon Chia Seed Muffins recipe from my cookbook.

I wanted to bring another classic muffin recipe into the blog and a bakery home to you because these are just so delightful.

baked lemon poppy seed muffins

About this Lemon Poppy Seed Muffins Recipe

Lemon and poppy seeds are a classic combo for muffins (and cake! See this Lemon Poppy Seed Cake recipe). For a twist, you can also try Orange Muffins with Poppy Seeds.

This is the type of muffin that first comes to mind when baking breakfast treats for company or wanting to do something a little more special than Healthy Banana Muffins.

Like my other healthy muffins recipes, this lemon poppy seed muffin recipe has some healthy additions and swaps:

  • Nonfat Greek yogurt in place of some of the butter, both for added protein and for less fat and calories.
  • Swapping half of the all-purpose flour for white whole wheat flour, adding additional fiber and protein.
  • Lesser amount of sugar than typical sweet muffin recipes, while still being a treat.
healthy lemon poppy seed muffins stacked with glaze

How to Make Lemon Poppy Seed Muffins

Muffins are probably my favorite thing to bake.

They are so easy and satisfying to whip up, and they make a great on-the-go breakfast or snack.

Grab some lemons and your muffin tin, and get ready to zest, juice, and go!

The Ingredients

  • Lemon. These muffins are loaded with zest and fresh lemon juice to deliver the perfect amount of lemon punch.


Blend the lemon zest into the sugar by rubbing the zest and sugar together with your fingers until moistened. This activates the zest’s oils and intensifies the flavor.

  • While Whole Wheat Flour. I use half white whole wheat flour and half all-purpose flour. The whole wheat flour is an undetectable healthy swap in to add more nutrients to the muffins. You can use entirely all-purpose flour if you prefer.
  • Poppy Seeds. Add both texture and flavor, and perfect pairing with lemon in muffins.
  • Greek Yogurt. These lemon poppy seed muffins are made with plain, non-fat Greek yogurt, another easy, healthy swap in baked goods, instead of sour cream or more butter.


Use room temperature yogurt, otherwise the melted butter may resolidify due to the cold yogurt.

  • Eggs. The binders. Be sure they are room temperature.
  • Butter. Some fat is needed for the muffins to be fluffy and the ingredients to properly combine, plus it adds amazing flavor, of course. This recipe has 4 tablespoons total.
  • Vanilla. Got to have vanilla in any baked good, IMHO. I strongly recommend pure vanilla extract, as the flavor really makes a difference.
  • Glaze. The lemon poppy seed muffin glaze is simple and sweet with lemon juice and powdered sugar.


Sift your powdered sugar to deliver a lump-free glaze.

The Directions

lemon poppy seed muffin ingredients in a mixing bowl
  1. In a large mixing bowl, whisk together the dry ingredients.
lemon zest and sugar in a large mixing bowl
  1. Zest lemon over sugar in a medium bowl, and rub the two together with your fingers until moist and fragrant.
wet ingredients for lemon poppy seed muffins in a large mixing bowl
  1. Add the wet ingredients and whisk until smooth.
whisking together lemon poppy seed muffin recipe
  1. Pour wet ingredients into the dry.
mixing lemon poppy seed muffin healthy recipe
  1. Stir gently until the flour disappears.
lemon poppy seed muffins on a cooling rack
  1. Bake lemon poppy seed muffins at 350 degrees F for 18 to 20 minutes.
lemon poppy seed muffins with yogurt on cooling rack
  1. Whisk together the lemon juice and powdered sugar to make the glaze, then drizzle over the cooled muffins. ENJOY!

Storage Tips

  • To Store. Store muffins in a paper towel-lined airtight container at room temperature on counter for up to four days.
  • To Freeze. Freeze muffins in an airtight, freezer-safe storage container for up to three months. Thaw and enjoy as desired. I like to individually wrap the muffins first, so I can use them for quick breakfasts and snacks.

Storage Tips

For even more tips on storing your leftovers, check out this post on How to Store Muffins.

What to Serve with Lemon Poppy Seed Muffins

Lemon poppy seed muffins are a tasty snack or grab ‘n’ go breakfast, or can be the sweet element in your brunch spread. Here are a few favorite breakfast and brunch menu items to serve with your muffins:

  • Muffin Pan. A must-have tool for making muffins. This one comes with a cover so you can take them to go!
  • Large Cookie Scoop. For scooping muffin dough, making for even baking and a better rise.
  • Nesting Mixing Bowls. This set of glass mixing bowls have a size for every cooking or baking need.

Muffin Tin

Get my tried-and-true, favorite muffin pan. Even heat distribution for even baking, and easy to clean.

yummy healthy lemon poppy seed muffins

Jump into spring (or dream of spring) with these perfect lemon poppy seed muffins!

Frequently Asked Questions

Do I Need to Soak the Poppy Seeds for Poppy Seed Muffins?

No, poppy seeds do not need to be soaked prior to baking lemon poppy seed muffins.

Do Poppy Seeds Add Flavor?

Poppy seeds add both flavor and texture. Their flavor is a bit fruity and nutty. It’s mild and pleasant.

Are Lemon Poppy Seed Muffins OK to Eat?

Poppy seeds are good sources of protein and fiber, and rich in B-complex vitamins, calcium, and magnesium. You would use food-grade poppy seeds and the entire recipe only has 2 tablespoons; these muffins are absolutely safe to eat for most people. (This is not medical advice; if you have concerns, please speak with your doctor.)

Do I Cool Muffins in the Tin?

For tender muffins, let cool in the pan for 5 minutes, then carefully lift the muffins out of the pan and transfer them to a wire rack to cool completely. If you let them cool completely in the muffin tin, they will steam and get soggy.

Lemon Poppy Seed Muffins

5 from 1 vote
Bright, zingy, and moist lemon poppy seed muffins. Made with healthy ingredients and a light glaze, they're better than a bakery!

Prep: 10 minutes
Cook: 20 minutes
Total: 30 minutes

Servings: 12 muffins


  • 4 tablespoons unsalted butter
  • 1 cup white whole wheat flour or whole wheat pastry flour or all-purpose flour
  • 1 cup all-purpose flour
  • 1 1/2 teaspoons baking powder
  • 1/4 teaspoon baking soda
  • 1/2 teaspoon kosher salt
  • 2 tablespoons poppy seeds
  • 3/4 cup granulated sugar
  • 3/4 cup nonfat plain Greek yogurt at room temperature
  • 2 large eggs at room temperature
  • 1 tablespoon lemon zest from about 3 lemons
  • 1/4 cup freshly squeezed lemon juice from the lemons above
  • 2 teaspoons pure vanilla extract


  • 1 1/2 tablespoons lemon juice from the lemons above
  • 3/4 cup powdered sugar sifted if lumpy


  • Preheat the oven to 350 degrees F. Coat a muffin tin with nonstick spray or line with paper liners. In a small bowl, melt the butter. Set aside to cool to room temperature.
  • In large bowl, whisk together the whole wheat flour, all-purpose flour, baking powder, baking soda, salt, and poppy seeds. Set aside.
  • Place the sugar in a medium bowl and add the lemon zest (zest the lemons directly over the bowl to capture their flavorful oils). With your fingers, rub the two together until the sugar is moist and fragrant. Add the yogurt, eggs, lemon juice, vanilla, and melted butter. Whisk until smooth.
  • Make a well in the center of the dry ingredients, then carefully pour in the wet ingredients. With a spatula or wooden spoon, mix gently just until the flour disappears. The batter will be thick.
  • With a scoop, divide the batter evenly between the muffin cups (they’ll be 2/3 to 3/4 of the way full).
  • Bake lemon poppy seeds muffins for 18 to 20 minutes, or until toothpick inserted in the center of a muffin comes out clean. Let cool in the pan for 5 minutes, then carefully lift the muffins out of the pan and transfer them to a wire rack to cool completely (this will keep the muffins from steaming in the pan and getting soggy).
  • While the muffins cool, make the glaze: Place the lemon juice and powdered sugar in a small bowl and whisk briskly until smooth. Add more powdered sugar or lemon juice as needed so that your glaze is a pourable consistency. Drizzle over the cooled muffins.



Adapted from the Lemon Chia Seed Muffins in my cookbook.
  • TO STORE: Store muffins in a paper towel-lined airtight container at room temperature on counter for up to four days.
  • TO FREEZE: Freeze muffins in an airtight, freezer-safe storage container for up to three months. Thaw and enjoy as desired. I like to individually wrap the muffins first, so I can use them for quick breakfasts and snacks.


Serving: 1muffin with glazeCalories: 212kcalCarbohydrates: 37gProtein: 5gFat: 5gSaturated Fat: 3gPolyunsaturated Fat: 1gMonounsaturated Fat: 1gTrans Fat: 0.2gCholesterol: 38mgPotassium: 122mgFiber: 2gSugar: 21gVitamin A: 157IUVitamin C: 3mgCalcium: 72mgIron: 1mg

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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    1. Hi Jill! You should definitely be able to make them into mini muffins but I haven’t tested it out myself so I can’t say for sure how long. I would just keep an eye on them around 10 minutes. Would love to know how they come out if you decide to experiment!