Healthy Lemon Poppy Seed Muffins with Almond Flour are fluffy, bright and full of delicious flavor. Using simple ingredients they are easy to make and a perfect way to start your day.

There's nothing like waking up to fresh muffins in the morning. However, if they're not being made for you this recipe is the perfect one to make.
It's a simple recipe so it doesn't take too much time to make. Even though they're easy to make, each muffin is bursting with lemon and the poppy seeds!
The flavor of the muffins are clearly off the charts but the texture is right there with it. The muffins are light and fluffy but also sturdy enough to hold in your hand.
Whether it's the beginning of Spring or the middle of Winter, these muffins never fail to brighten my day (and tasty incredibly delicious too)!
Ingredient Notes
- Gluten Free All Purpose Flour - You can also use regular All Purpose flour for this recipe if you prefer.
- Almond Flour - the Almond Flour adds the perfect texture to the muffins. It helps keep them light with a crumbly texture.
- Organic Granulated Cane Sugar - Regular Granulated Sugar will work just as well. You don't have to use organic, whatever your preferred brand will yield the same result.
- Coconut Oil - I love the slight coconut flavor that coconut oil adds when baking with it. It's easy to use and a healthier alternative to vegetable oil.
- Egg - Use a large egg for this recipe. However, an extra large egg will turn out okay if that's all you have on hand.
- Butter - I use salted butter but you can use unsalted and add a pinch of salt to the batter.
- Milk - Almond milk is used in this recipe but you can replace with regular milk.
- Lemon juice - No zest in this recipe, just the juice! This keeps the recipe easy and no zest chunks get stuck in your teeth.
- Vanilla Extract - Just a little goes a long way for this recipe!
- Poppy Seeds - It wouldn't be Lemon Poppy Seed Muffins without these π You should be able to find them at your local grocery store or on Amazon (linked).
- Baking Powder and Baking Soda - These two work together to give these muffins the perfect rise and texture.

What's the perfect muffin texture?
What is your ideal texture for a muffin? In my opinion, the perfect muffin is light and a little crumbly BUT it holds up on it's own without falling apart in your hand.
These muffins stand tall and don't sink after taking them out of the oven. Which is also the worst and you won't have to worry about that in this recipe.
How to Make the BEST Healthy Lemon Poppy Seed Muffins
- Preheat the oven to 400 degrees F
- Whisk together the egg and sugar until light and fluffy
- Add in the butter, coconut oil, milk, lemon juice and vanilla extract
- Mix until fully combined
- Fold in the flour(s), baking powder and baking soda
- Mix until fully combined then incorporate the poppy seeds
- Let the batter rest for 30 minutes to 1 hour
- Using about ΒΌ cup, fill every other muffin liner with batter. The liners should be filled to just below the top
- Bake for 8 minutes then reduce the oven temperature to 350 degrees F. Bake for an additional 8-10 minutes
- The muffins are done when slightly golden on top and a toothpick comes out clean
- Let cool and enjoy!

Key factors to making these muffins perfect
- Prepping Your Muffin Tin - make sure you line your muffin tins with greased muffin liners. i use coconut oil spray for all of my sweet recipes.
- Muffin Pan Placement - spread the muffins out and don't bake any next to each other. by baking in every other muffin tin, this gives the muffins room to breathe and rise high to create the dome top we all love and want.
- Lemon Juice - Some recipes only call for lemon zest in the recipe, but I prefer to use only lemon juice. It adds the perfect punch of lemon without any chunks of zest.


Frequently Asked Questions
Yes! The regular all purpose flour will give you the same result.
You can also use all gluten-free all purpose flour or regular all purpose in place of the ΒΌ cup of almond flour if you don't have any on hand.
I use almond milk but you can also use regular milk or the milk you prefer. The only milk I don't recommend using is coconut milk. That will change the texture and be a strong flavor to add.
Yes! You can add fruit such as blueberries, raspberries and blackberries. I recommend using fresh so that the batter consistency remains the same. You can also get creative with different flavorings/extracts.
To make 12 muffins just double the measurements of each ingredient. For baking, still bake each muffin in every other tin. The spacing gives the muffins room to rise. You can do this by baking two trays at once or one at time.
Store in an airtight container for up to 5 days or in the freezer for up to 1 month.
If you liked this healthy lemon poppy seed muffins recipe, try these!
- Fluffy Bakery Style Banana Muffins
- Coffee Cake Muffins (Gluten Free Friendly)
- Bakery Style Pumpkin Muffins
- Healthy Cornbread Muffins
If you try this recipe, please consider leaving a rating and comment at the end of this blog post. It is incredibly helpful to my business and to your fellow readers!

Healthy Lemon Poppy Seed Muffins with Almond Flour
Ingredients
- 1 large egg
- Β½ cup granulated organic cane sugar
- 1 tbsp coconut oil melted and cooled
- ΒΌ cup salted butter melted and cooled
- 1 lemon juice only
- 1 tsp vanilla extract
- Β½ cup milk room temperature
- 1 cup gluten free flour
- ΒΌ cup almond flour
- Β½ tbsp baking powder
- ΒΌ tsp baking soda
- 1 tbsp poppy seeds
Instructions
- Preheat the oven to 400 degrees F
- Whisk together the egg and sugar until light and fluffy
- Add in the butter, coconut oil, milk, lemon juice and vanilla extract
- Mix until fully combined
- Fold in the flour(s), baking powder and baking soda
- Mix until fully combined then incorporate the poppy seeds
- Let the batter rest for 30 minutes to 1 hour
- Using about ΒΌ cup, fill every other muffin liner with batter. The liners should be filled to just below the top
- Bake for 8 minutes then reduce the oven temperature to 350 degrees F. Bake for an additional 8-10 minutes
- The muffins are done when slightly golden on top and a toothpick comes out clean
- Let cool for 10 minutes and enjoy!
One question I have is if I could substitute the almond flour with another type of flour, as I have a nut allergy. What do you suggest? Thank you for sharing this recipe, it's definitely a keeper!
Yes! You can substitute the almond flour for regular all purpose flour or gluten free as well. I hope you enjoy!
Such fluffy and tasty muffins, and the tips really helped too!
I made them for breakfast, and they are amazing. Soft and rich in flavor.
Will make them again as they are super easy to make.
Thank you for the recipe
These muffins are fantastic! Super delicious and easy to make!
Thank you so much! I'm so glad you liked it:)