These Healthy Lemon Poppyseed Muffins are light, fluffy, and bursting with lemon flavour! With a soft center and a crispy top, these sweet and tangy muffins are perfect for breakfast!

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

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 Poppyseed Spelt Pancakes, so naturally I decided it would be the right move to stock my kitchen full of the best lemon poppyseed muffins.

These muffins are crispy on top, soft and fluffy in the middle, slightly tangy from the greek yogurt and slightly tart and sweet all at the same time. Like hello muffin perfection!

how to make lemon poppy seed muffins

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 mean 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.

healthy lemon poppy seed muffins

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 regular flour)
  • Organic cane sugar (not too much, but just the right amount to make them sweet)
  • PLENTY of lemon and poppy seeds!

How to make lemon poppy seed muffins

Everyone rejoice, because healthy lemon poppy seed muffins are easy to make! *cue applause.*

Here’s what you’re gonna do: mix together the dry ingredients in one bowl, and the wet ingredients in another bowl. Then, mix both of those together, and spoon the batter in your muffin pan.

healthy lemon poppy seed muffins

A few notes on the recipe

These healthy lemon poppy seed muffins are very versatile when it comes to ingredients. If you’d like to make them gluten-free, simply use a 1-1 gluten-free flour blend.

If you’d like to make them dairy-free, use a plant-based yogurt (I like coconut yogurt) and coconut oil in place of the butter.

I haven’t tested out a vegan version of this recipe so I can’t say how they would turn out if you used a flax egg in place of the egg, but I imagine that they would turn out well! If you would prefer to make this recipe into a loaf, you can use an 8×4 inch loaf pan and adjust the baking time to bake for 45-60 minutes.

a healthy lemon poppyseed muffin with a bite in it

More muffin recipes to try

clock clock iconcutlery cutlery iconflag flag iconfolder folder iconinstagram instagram iconpinterest pinterest iconfacebook facebook iconprint print iconsquares squares iconheart heart iconheart solid heart solid icon
healthy lemon poppy seed muffins

Healthy Lemon Poppyseed Muffins

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


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


  • 1 3/4 cup Spelt flour (can sub regular flour, 11 gluten-free flour, or half whole-wheat & half regular)
  • 1/2 cup organic cane sugar
  • 1 tsp baking powder
  • 3/4 tsp baking soda
  • 1/4 tsp salt
  • 2 tbsp lemon zest
  • 2 tbsp poppy seeds
  •  1 cup greek yogurt (can sub dairy-free yogurt)
  • 1/3 cup freshly squeezed lemon juice
  • 1 egg
  • 1/3 cup butter or coconut oil, melted and cooled.
  • 1 tsp vanilla extract


  1. Preheat the oven to 400 degrees F and line a muffin pan.
  2. Mix all the dry ingredients together in a bowl. Mix all the wet ingredients together in a separate bowl.
  3. Pour the dry ingredients into the wet and mix until combined.
  4. Spoon the batter into the muffin pan filling 3/4 of the way full.
  5. Bake for 17-20 minutes or until a toothpick comes out clean.


Some brands of yogurts may be thicker than others. If yours is very thick, add 2-3 tbsp of milk or water to your batter if it having trouble incorporating.


  • Serving Size: 1 muffin
  • Calories: 165
  • Sugar: 9g
  • Sodium: 95mg
  • Fat: 6g
  • Saturated Fat: 3g
  • Carbohydrates: 23g
  • Fiber: 2g
  • Protein: 5g

Keywords: how to make lemon poppy seed muffins, healthy lemon poppy seed muffins

If you tried these Healthy Lemon Poppyseed 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!