These Healthy Lemon Poppy Seed Muffins are light, fluffy, and bursting with lemon flavour! They’re soft and fluffy and perfect for a healthy breakfast, snack or treat!

a lemon poppy seed muffin with a bite taken out of it

The best lemon poppy seed muffins

Can we just take a minute to appreciate how amazing this duo of lemon and poppy seed is? I don’t know about you but I’m a BIG FAN.

Especially when it comes to baked goods, my eyes light up whenever I hear the words…”lemon poppy seed.” Heck, I’ve made Lemon Poppyseed Bliss Balls and Lemon Poppy seed Spelt Pancakes, so naturally, I decided it would be the right move to stock my kitchen full of the best lemon poppy seed muffins.

So what makes for the best lemon poppy seed muffins?

First off, I think a good muffin recipe should always be easy to make. Which means you won’t need any mixers or fancy kitchen gadgets to make these. (Ok, you will need a muffin pan though.)

I love these muffins because they’re filled with fresh, light healthy ingredients. Which makes them perfect for breakfast, a snack or a dessert.

Let’s take a closer look at what we’ve got going on in these muffins, shall we?

  • Greek yogurt for some added protein
  • Spelt flour for healthy whole grains (though you can easily substitute gluten-free flour or all-purpose flour if you prefer)
  • Organic cane sugar (not too much, but just the right amount to make them sweet)
  • PLENTY of lemon and poppy seeds!

Why you’ll love this recipe

  • Easy to make. These muffins are super easy to make right in a mixing bowl without having to use a stand mixer or hand mixer. They also have minimal cleanup!
  • Simple ingredients. These lemon poppy seed muffins are made with simple ingredients for a healthier muffin that’s not too sweet.
  • Freezer-friendly. Made too many muffins? No problem! These muffins store well in the freezer for up to 2 months.

How to make lemon poppy seed muffins

Step 1

Whisk together the egg, greek yogurt, avocado oil and vanilla extract in a large mixing bowl until well combined. In a separate bowl, mix together the sugar and lemon zest.

Step 2

Whisk the lemon sugar into the bowl of wet ingredients until combined. Then add the flour, baking powder, baking soda and salt and gently fold everything together.

Step 3

Add the poppy seeds to the muffin batter and gently fold them together again to combine.

Step 4

Line a muffin pan with muffin liners and bake the muffins in a preheated oven at 350 degrees F for 16-20 minutes or until a toothpick comes out clean. Once the muffins are baked and cooled you can optionally add the lemon glaze on top, though it’s not necessary and the muffins are delicious as is!

How to store

Store these muffins in an airtight container on the countertop for up to 5 days or in the fridge for up to 7 days.

These muffins are also freezer-friendly. To freeze the muffins place them in a freezer-safe bag and freeze for up to 2 months. To defrost the muffins let them thaw on the countertop.

Tips for making lemon poppy seed muffins

  • Mix up the flour. If you can’t find spelt flour, you can use all-purpose flour a 1-1 gluten-free flour blend, or half whole-wheat flour and half all-purpose flour.
  • Don’t substitute with almond flour or coconut flour. These types of flour cannot be used in an equal ratio to wheat flour as they absorb much more liquid. The muffins won’t turn out properly with these flours.
  • Make them dairy-free. To make these muffins dairy-free, use plant-based yogurt (like coconut yogurt) and plant-based milk.
  • Don’t overmix the batter. This will create dense muffins. Just gently mix until everything is incorporated.
  • Make it a lemon poppy seed loaf. To make this recipe into a loaf, use an 8×4 inch loaf pan and bake for 45-60 minutes.

More muffin recipes to try

lemon poppy seed muffins with lemon glaze

If you tried these Healthy Lemon Poppy seed Muffins or any other recipe on the blog let me know how you liked it by leaving a comment/rating below! Be sure to follow along on PinterestInstagram and Facebook for even more deliciousness!

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a lemon poppyseed muffin with a bite taken out of it

Healthy Lemon Poppy seed Muffins

  • Author: Jessica Hoffman
  • Prep Time: 10 minutes
  • Cook Time: 20 minutes
  • Total Time: 30 mins
  • Yield: 12 muffins 1x
  • Category: Breakfast, Snack, Dessert
  • Method: Bake
  • Cuisine: American
  • Diet: Vegetarian


These healthy lemon poppy seed muffins are seriously just the BEST. Soft and fluffy, sweet and tangy, they’re the perfect breakfast treat!


Units Scale


  • 1 3/4 cups Spelt flour (can sub all-purpose flour, 1-1 gluten-free flour )
  • 1 tsp baking powder
  • 3/4 tsp baking soda
  • 1/4 tsp salt
  • 2 tbsp lemon zest
  • 1/2 cup organic cane sugar
  • 1 egg
  • 1 cup greek yogurt (can sub dairy-free yogurt)
  • 1/4 cup milk
  • 1/3 cup freshly squeezed lemon juice
  • 1/3 avocado oil (can sub any neutral-tasting oil)
  • 1 1/2 tsp vanilla extract
  • 3 tbsp poppy seeds

Lemon glaze

  • 1/2 cup powdered sugar
  • 1 tbsp lemon juice


  1. Preheat the oven to 350 degrees F and line a muffin pan.
  2. Mix the sugar and lemon zest together in another bowl. 
  3. In a large mixing bowl, whisk together the egg, Greek yogurt, milk, lemon juice, avocado oil and vanilla extract.
  4. Add the lemon sugar to the wet ingredients and mix until the sugar is dissolved. 
  5. Add the flour, baking powder, baking soda and salt into the bowl of wet ingredients and gently mix just until combined. Don’t overmix. 
  6. Add the poppy seeds and gently mix again. 
  7. Spoon the batter into the muffin pan filling 3/4 of the way full.
  8. Bake for 16-20 minutes or until a toothpick comes out clean. 
  9. To make the glaze mix together the powdered sugar and lemon juice, then use a spoon to drizzle the glaze onto the muffins. (Let the muffins cool before adding the glaze.) 


The lemon glaze is optional. These muffins are delicious too without it!

Store in an airtight container on the counter for 5 days or in the fridge for 7 days.


  • Serving Size: 1 muffin
  • Calories: 150
  • Sugar: 9g
  • Fat: 6g
  • Carbohydrates: 23g
  • Fiber: 2g
  • Protein: 5g

Keywords: healthy lemon poppy seed muffins, easy lemon poppy seed muffins