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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

Why You’ll Love This Easy Lemon Poppy Seed Muffin Recipe

  • Tastes Like Sunny Days. 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.
  • Easy and Classic. Lemon and poppy seeds are a classic combo for muffins and Lemon Poppy Seed Cake. (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 last minute company, but still wanting to do something a little more special than Healthy Banana Muffins.
  • Well Plated Tweaks. 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, half of the all-purpose flour for white whole wheat flour, and less sugar. Win!
baked lemon poppy seed muffins

5 Star Review

“Best lemon poppyseed muffin I’ve ever had!”

— Maggie —

How to Make Lemon Poppy Seed Muffins

The Ingredients

  • Lemon. These muffins are loaded with zest and fresh lemon juice to deliver the perfect amount of lemon punch.
  • White Whole Wheat Flour. I use half white whole wheat flour and half all-purpose flour, but you can use entirely all-purpose flour if you prefer.
  • Poppy Seeds. Poppy seeds add both flavor and texture. Their flavor is a bit fruity and nutty. It’s mild and pleasant.
  • Greek Yogurt. These lemon poppy seed muffins are made with plain, non-fat Greek yogurt instead of sour cream or more butter. They make these muffins extra moist!
  • 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.
  • 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.

The Directions

lemon poppy seed muffin ingredients in a mixing bowl
  1. Whisk. In a large mixing bowl, whisk together the dry ingredients.
lemon zest and sugar in a large mixing bowl
  1. Rub. 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. Mix. Add the wet ingredients and whisk until smooth.
whisking together lemon poppy seed muffin recipe
  1. Combine. Pour wet ingredients into the dry.
mixing lemon poppy seed muffin healthy recipe
  1. Fold. Stir gently until the flour disappears.
lemon poppy seed muffins on a cooling rack
  1. Bake. Bake lemon poppy seed muffins at 350 degrees F for 18 to 20 minutes.
lemon poppy seed muffins with yogurt on cooling rack
  1. Glaze. 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. (For even more tips on storing your leftovers, check out this post on How to Store Muffins.)
  • 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.
healthy lemon poppy seed muffins stacked with glaze

What to Serve with Lemon Poppy Seed Muffins

Recipe Tips and Tricks

  • Release the Lemon Oil. 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.
  • Let the Yogurt Come to Room Temp. Use room temperature yogurt, otherwise the melted butter may resolidify due to the cold yogurt.
  • Don’t Use Lumpy Powdered Sugar. Sift your powdered sugar to deliver a lump-free glaze.
  • Remove From the Muffin Pan. 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.
yummy healthy lemon poppy seed muffins

Lemon Poppy Seed Muffins

5 from 4 votes
This easy recipe makes bright, zingy, and moist lemon poppy seed muffins that taste better than a bakery. Don't skip the zippy lemon glaze!

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!

  1. Best lemon poppyseed muffin I’ve ever had! I’ve made the lemon chia seed muffins from Erin’s cookbook and they are equally perfect!5 stars

  2. Looks amazing…lemon is my favorite flavor! I was wondering if you could use Einkorn flour in this recipe in place of both AP and WWW flour. Since there is a good amount of WWW the amount of liquid I’m guessing would not need to be altered. Thoughts? Thank you so much!

    1. Hi Pagie, I’m not familiar with Einkorn flour so I can’t say. If you decide to experiment, let me know how it goes!

  3. I made these for a church event and they were DELICIOUS. Everyone loved them and I brought home an empty bowl! I’m making another batch right now for those who requested more muffins. Thanks for a great recipe!5 stars

  4. I loved the taste of these and they were perfectly moist! I used plain Greek yogurt and some extra lemon juice in the batter. I also used less poppy seeds and sprinkled some sugar crystals on top of the muffins before baking. Really delicious, I will definitely make these again!5 stars

  5. Worked out perfectly. Light and fluffy. I love the texture and it has the right amount of sweetness. Happy with how these turned out! I made the recipe almost exactly, however I did add an extra teaspoon of lemon juice for some extra lemony taste. This was a hit with my kids. They love it. Thank you, Erin!5 stars