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These healthy lemon poppy seed muffins are a lighter twist on the classic recipe. Soft and moist on the inside and slightly browned on the outside. Plus they’re full of so much citrus flavor.

Looking for more healthy and delicious muffin recipes? Try these healthy oatmeal chocolate chip muffins, gluten-free pumpkin muffins, or healthy banana muffins next.

Healthier lemon poppy seed muffins iced on a counter
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The weather Gods have awakened and sent the most perfect late-spring day upon us at the end of February. It’s so magical. Typically, I look out my window to snow and gloom and today it’s pure sunshine and warmth. It’s 75 degrees in Columbus, Ohio to be exact. A record high! That means it’s never been this wonderful outside in the history of the universe on this specific date.

And I don’t know about you, but I think that deserves to be celebrated. And celebrations are coming in the form of healthier lemon poppy seed muffins today! ☀

I was going to wait a little bit longer to post this recipe but this day seemed so fitting. I love when the weather breaks because it means springtime and desserts full of lemon and citrus. It brings the color back into my life and I get a newfound inspiration from colorful food to share.

Healthier lemon poppy seed muffins batter in a glass bowl with a whisk in it

One of those colorful foods happens to be lemon! I have to admit I haven’t always been a fan of lemon desserts, but I’ve slowly fallen in love. My relationship status? Lemon.

Not really, because I just got engaged!!! Read more if you’re interested! But really, it’s so tasty and adds a zing to my tastebuds and a big burst of flavor when I take a bite.

I especially love it in the form of lemon poppy seed (see lemon poppy seed bread) because it reminds me of my dad. He would head out to the store on a Sunday and return with 6 giant lemon poppy seed muffins for my sisters and I. Waking up to those was pure heaven.

Though they were as big as my face and likely filled with tons of fat and oil. And since my metabolism doesn’t work in the ways it used to I wanted to recreate that memory, but add a healthy twist. Hence, healthier lemon poppy seed muffins.

Healthier lemon poppy seed muffins batter in muffin tin with paper cups

They’re healthier because they don’t require any oil or butter. They’re made with olive oil, coconut oil and Greek yogurt to give them a moist and delicious texture.

I absolutely love the addition of the olive oil in these healthier lemon poppy seed muffins because I think the flavors of lemon and olive oil are a match made in heaven. The key is to use really good olive oil. You will be able to taste it through the muffins so make sure you use a brand and variety you love. I prefer extra virgin olive oil!

However, if you aren’t into olive oil you can absolutely sub it out for all coconut oil. The muffins will turn out just as perfect, pinky promise.

bag of icing being squeezed onto healthier lemon poppy seed muffins

The poppy seeds don’t have an overt flavor to them but they provide the muffins with a crunchy texture and they look super pretty.

Another reason these healthier lemon poppy seed muffins look super pretty is because of the icing on top! You can omit it (I supposed), but it adds an extra zing of lemon and they look so pretty, like you spend hours baking them.

But the good news is they’re actually they’re super simple to make! No busting out the electric mixer or stand mixer, just a good old-fashioned whisk, and a little elbow grease.

You can use muffin liners for this recipe or you can skip them all together. Both are fine! These healthier lemon poppy seed muffins won’t stick to the sides of the liners and come out of the pan easily if you give them a good spray before adding the batter.

I’d recommend filling the muffin tins about ¾ of the way full. These muffins rise quite a bit so you don’t want them overflowing the top of the pan and baking unevenly.

Healthier lemon poppy seed muffins stacked in a carton on a counter with more muffins surrounding it

I also have a special trick when it comes to the oven temperature when I make muffins! I feel like I’ve been sharing this type a lot lately, probably because I’ve been a little obsessed with muffins lately. See: GF Chocolate Banana Muffins and Nutella Stuffed Banana Muffins. But the trick is simple! Bake the muffins for the first few minutes at a higher temperature (in this case 425°F) and then reduce the heat to 350°F and finish baking.

This technique allows the muffins to rise quickly. and create the rounded dome look you see at bakeries. When you reduce the heat it allows the muffins to bake evenly through the rest of the way. Just set your timer to remember to turn it down and you’ll have perfect healthier lemon poppy seed muffins in under 15 minutes.

Glazed healthier lemon poppy seed muffins on a cutting board with lemon slices
Healthier lemon poppy seed muffins cut in half with the inside of the halves facing upward on a counter top

I like to eat mine in the mornings, but these healthier lemon poppy seed muffins are perfect any time of day! Especially on days like today,

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4.28 from 11 votes

Healthy Lemon Poppy Seed Muffins

Prep: 15 minutes
Cook: 15 minutes
Total: 30 minutes

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Servings: 12


  • 1 1/2 cups oat flour
  • 1/2 cup tapioca flour
  • 1/2 cup cane sugar
  • 2 1/2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 2 Tablespoons poppy seeds
  • 1/2 cup refined coconut oil melted
  • 2/3 cup plain Greek yogurt
  • 2 large eggs room temperature
  • 3/4 cup milk room temperature
  • 2 Tablespoons lemon zest (about 2 lemons)
  • 2 Tablespoons lemon juice (about 1 lemon)
  • 1 teaspoon vanilla extract
  • 1/4 teaspoon almond extract

Lemon Glaze and Icing

  • Juice from 1 lemon divided
  • 1/2 cup powdered sugar
  • 1/4 cup Greek yogurt


  • In a large bowl, whisk together the oat flour, tapioca flour, sugar, baking powder, baking soda, salt, and poppy seeds.
  • In another medium bowl, whisk together the melted coconut oil, eggs, sour cream, vanilla extract, almond extract, lemon zest, lemon juice, and milk.
  • Pour the wet mixture into the dry ingredients and use a rubber spatula to combine. Do not over mix.
  • Cover the bowl with plastic wrap or a towel and rest at room temperature for at least 20 minutes, or up to an hour. You can also place in the fridge overnight.
  • While it's resting, preheat the oven to 425°F. Line a muffin tin with one of these two options: 1) line with 12 paper liners or 2) line every other muffin tin with 6 paper liners and bake in 2 batches, which gives you taller muffin tops (I prefer option 2).
  • Use a large (2 oz) cookie scoop, or about 1/4 cup) to scoop the muffin batter into the prepared muffin tin. Be careful not to deflate the batter.
  • Bake for 8 minutes in the preheated oven then reduce the oven temperature to 350°F and continue to bake for 8-10 minutes. Be sure to set the temp back to 425 if you're baking in 2 batches.
  • Let them cool for 5 minutes in the pan then transfer the muffins to a cooling rack to cool another 20 minutes. While they're cooling, make the glaze. Whisk together the lemon juice, powdered sugar, and Greek yogurt. Drizzle on top of the muffins and serve.
Last step! If you make this, please leave a review letting us know how it was!

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Recipe Rating


  1. WholeYum says:

    These lemon poppyseed muffins looks so good! We would love to see the recipe on WholeYum!