Brighten up your mornings with Healthy Lemon Poppy Seed Muffins made with almond flour, Greek yogurt, and naturally sweetened with maple syrup. Enjoy with or without a delicate lemon glaze drizzled on top!

Another lemon favorites around here are these healthy lemon bars and healthy lemon poppy seed bread.

Healthy lemon poppy seed muffins with glaze and fresh lemon garnish on top.

I have yet to meet anyone who doesn’t love a muffin, which means these healthy lemon poppy seed muffins are for everyone. Especially YOU. I see you, lemon lovers!

As much as I love any kind of muffin, like these almond flour banana muffins, for most of the year, I wanted something a little lighter for spring.

Enter these delicious lemon-y muffins made with almond flour and flecked with poppy seeds!

They’re one of the healthy muffin recipes combining sweet and tart flavors, thanks to the maple syrup and Greek yogurt. The tang of course comes from double the lemon because we’re using the juice and the zest!

When I think of light and fluffy lemon muffins, I think of Mother’s day breakfasts, sunshine, and sipping on a fresh healthy strawberry smoothie or a healthy iced coffee.

Healthy lemon poppy seed muffin with a bite taken out of the one in front.

Whole wheat flour, like in these healthy lemon zucchini muffins is great, but even still a little too heavy for what I had in mind.

Using almond flour keeps them gluten-free, light, and fluffy. Greek yogurt and egg packs in the protein and moisture. And the maple syrup keeps them refined sugar-free.

The vibrant burst of fresh lemon and the flecks of poppy seeds are what will keep you coming back to this healthy recipe all season long!

You may also love to browse over 20 healthy almond flour recipes to never run out of ideas on what to bake next!

Ingredients You Will Need

These lemon poppy seed muffins are made for all lemon lovers! You’ve probably got everything you need in your kitchen already. Here is the list:

  • Eggs: Used for binding which is especially important when using gluten-free flour. Haven’t tried with a flax egg but I think it will work. Let me know.
  • Maple syrup: I love the maple and lemon flavor, however, honey and lemon also go hand in hand.
  • Greek yogurt: Use 2% or higher for richness and to achieve a nice thick batter. You can use flavored yogurt, like vanilla for a little extra taste.
  • Lemons: Double the lemon with zest and the juice! Freshly squeezed is best.
  • Vanilla extract: A flavor enhancer that enriches many baking recipes by bringing out the other flavors.
  • Leavening agents: Baking powder and baking soda will give these muffins a beautiful rise. Important when using almond flour, it needs a little extra help!
  • Salt: Just to bring out some of the other flavors in the muffin and to balance out any sweetness.
  • Almond flour: Blanched and super fine. OK, so remember this isn’t almond meal.
  • Poppy seeds: Because healthy lemon poppy seed muffins!
  • Cooking spray: I use Misto, but you use what you have on hand.

For the glaze

  • Powdered sugar: If refined sugar doesn’t bother you, go ahead and use the confectioner’s sugar. If you want a sugar-free alternative, do what I do and use powdered erythritol.
  • Lemon juice: Fresh is best, but bottled works too.
Almond flour, Greek yogurt, eggs, lemons, maple syrup, poppy seeds.

How to Make Healthy Lemon Poppy Seed Muffins

This easy recipe comes together with 10 minutes of prep time using just one mixing bowl! While muffins are baking or cooling, make the lemon glaze and you don’t even have to wait long for muffins to cool off in order to drizzle it on them.

Here’s how it’s done.

  • Make the base of the batter. Combine eggs, maple syrup, yogurt, zest and lemon juice, vanilla extract, baking powder, baking soda, and salt into a large mixing bowl. Whisk until well combined and smooth. There should be no lumps.
  • Add in the flour and poppy seeds. Measure the almond flour by using the spoon and level method and add it to the batter. Then, follow that with the poppy seeds and stir gently using a spatula. Mix everything well.
  • Divide and bake. Use an ice cream scoop to add even amounts of batter to prepared muffin tin lined with parchment liners. Bake on the middle rack of a preheated 350-degree oven for 20-22 minutes until golden brown. Check for doneness by inserting a toothpick into the center. If it comes out clean, they’re ready!

Best way to scoop muffin batter? With ice cream scoop or cookie scoop! Dividing the batter equally into each crevice means they’re all going to be the same size. You need this to ensure each one is baked evenly.

  • Drizzle with lemon glaze. Allow the muffins to cool for 10 minutes during which time you’ll make a glaze. Whisk powdered sugar and lemon juice in a small bowl. Once they’ve cooled a bit, drizzle each of them with some of the healthy lemon glaze and enjoy!

Other glaze options: So many flavors pair well with lemon! A raspberry, strawberry, or blueberry glaze would be amazing! You could also try a honey or maple syrup glaze.

A Few Notes on the Recipe

  • Only use liquid sweeteners. This recipe is pretty flexible in terms of what kind of sweetener you use, as long as it’s liquid. Using a dry sweetener will throw batter consistency off.
  • Regular yogurt. Use it if that’s what you have. It is thinner and will affect the liquid to dry ratio. In this case, you might need to add 1/3 cup of extra almond flour to keep it thick enough.
  • Bake on the middle rack: I recommend not to bake on lower rack because almond flour has high oil content and tends to burn fast. Just follow the recipe.
  • Muffins can be made ahead. Prepare the batter, minus the baking soda and baking powder, up to a day in advance. Cover the bowl and leave it in the fridge overnight. When you’re ready to bake the healthy lemon poppy seed muffins, add the leavening agents back in, stir it and continue as per directions.

Turn it into a cupcake! Top it with a Greek yogurt frosting or a thick and luscious healthy cream cheese frosting.

Can I Use Any Other Type of Flour?

Not in this recipe. Almond meal is the closest thing that might work, but I find it to be heavier and more robust, which will lead to muffins being less light and fluffy.

If you give it a try, please let me know how they turn out.

How Do I Store These Muffins?

If you have any uneaten muffins, keep them at room temperature for up to 3 days. They’re great for snacking, grabbing a quick breakfast, or even as an after-school snack. Keep them close by for everyone to enjoy!

I don’t think you’ll have any left at this point, but if you do, transfer them to the fridge for another couple of days.

Can I Freeze Muffins?

You bet! These muffins freeze very well. Once completely cooled, transfer them to a freezer-friendly Ziploc bag. Keep layers separate with parchment paper so they don’t stick together when frozen.

Healthy lemon poppy seed muffins with glaze on counter.


Can I use sour cream instead of yogurt?

Sour cream and Greek yogurt can be used interchangeably in most cases. They both replace the oil or butter used in baking recipes and they both lend a tang and tartness. The acid reacts with the leavening agents helping baked goods to rise.

There is a nutritional difference in that Greek yogurt has more protein and less fat than sour cream does.

How can I make mini muffins?

Divide batter into mini muffin tins and bake them for about 13 minutes. All ovens differ, so to be safe check in on them at the 10-minute mark.

You could also turn this versatile recipe into lemon poppy seed bread!

How can I jazz up these muffins?

Love the pairing of berries and lemon! Toss some blueberries into the batter similar to almond flour blueberry muffins or whole wheat healthy lemon blueberry muffins. You could also add cherries, raspberries, and strawberries!

Add a swirl of your favorite jam into the batter, or add a dollop in the middle.

More Lemon Recipes to Try

Alternately, browse all my favorite healthy muffin recipes!

Looking down at healthy lemon poppy seed muffins with glaze and lemon slice.
Healthy lemon poppy seed muffins unwrapped with icing and fresh lemon.

Healthy Lemon Poppy Seed Muffins

Brighten up your mornings with these Healthy Lemon Poppy Seed Muffins. Enjoy with or without a delicate lemon glaze drizzled on top!
5 from 4 votes
Servings 12 muffins
Calories 260
Prep Time 10 minutes
Cook Time 20 minutes
Cooling Time 10 minutes
Total Time 40 minutes


For Muffins:

For Lemon Glaze:

  • 1/4 cup powdered sugar I use eryhtritol
  • 1 tbsp lemon juice or water more if needed


  • Preheat oven to 350 degrees F. Line 12 muffin tin with parchment paper muffin liners (highly recommended) and spray with cooking spray. Set aside.
  • In a large bowl, add eggs, maple syrup, yogurt, lemon zest and juice, vanilla extract, baking powder, baking soda and salt. Whisk very well until combined and no lumps.
  • Add almond flour (make sure to level the top with a knife and do not pack) and poppy seeds. Stir gently with spatula until well mixed.
  • Using an ice cream scoop, divide batter between 12 openings of previously prepared muffin tin. Bake for 20-22 minutes on the middle rack or until toothpick inserted in the center comes out clean and muffins are golden brown.
  • Remove from the oven and let cool for 10 minutes. While muffins are cooling, make glaze by whisking powdered sugar and lemon juice in a small bowl. Drizzle over muffins and enjoy!

Freezing: Freeze in layers with parchment paper between, in a large freezer bag for up to 3 months.


    • Store: Store muffins at room temperature for 2-3 days or within the refrigerator for 5 days.
    • Freeze: Freeze in layers with parchment paper between, in a large freezer bag for up to 3 months.
    • Don’t substitute flour or liquid sweetener: Almond meal might work, just muffins will be more dense and rise less. If you use dry sweetener, batter consistency will be off.
    • Regular and other yogurt: You can use plain regular (not Greek) yogurt, however might have to add 1/4 cup extra almond flour since it contains more liquid. Can also use flavored yogurt. The goal is to bring batter to consistency in the photos – thicker than for pancakes.
    • Fresh lemon juice is the best but bottled will work as well.


    Serving: 1muffin | Calories: 260kcal | Carbohydrates: 20g | Protein: 10g | Fat: 18g | Saturated Fat: 2g | Trans Fat: 1g | Cholesterol: 42mg | Sodium: 164mg | Fiber: 4g | Sugar: 13g
    Course: Muffins and Quick Breads
    Cuisine: North American
    Author: Olena Osipov
    Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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    About Olena

    Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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    1. Thank you so much for some amazing recipes. I’m a faithful follower!!

      Is there an alternative to Almond Flour? I’m not able to find it in Montenegro. What mods would I make for regular flour?

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