Gluten-Free Lemon Poppy Seed Muffins are fluffy, bright and full of delicious flavor. Using simple ingredients they are easy to make and a perfect way to start your day.

Lemon Poppy Muffin with a bite taken out.

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 flavor 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.

Ingredient Notes

  • Gluten Free All Purpose Flour – You can also use regular All Purpose flour for this recipe if you prefer.
  • Granulated Sugar
  • 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 – Whole milk is used in this recipe but you can replace with your preferred milk.
  • Lemon zest and juice
  • Vanilla Extract
  • Poppy Seeds – It wouldn’t be Lemon Poppy Seed Muffins without these 🙂 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.
Ingredients measured out in bowls to make gluten free lemon poppy seed muffins.

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.

See the FAQ section for tips on baking bakery style muffins that rise tall with a dome top.

How to Make Gluten-Free Lemon Poppy Seed Muffins

  1. Preheat the oven to 400 degrees F
  2. Add the granulated sugar and lemon zest to a large mixing bowl
  3. Rub the zest into the sugar to release the oils using your fingers
  4. Add the butter, eggs, milk, greek yogurt and vanilla extract
  5. Whisk until combined
  6. Add in the lemon juice and poppy seeds
  7. Mix until fully combined
  8. Fold in the flour, baking powder and baking soda
  9. Mix until just combined
  10. Let the batter rest for 30 minutes to 1 hour
  11. Using a 2 tbsp cookie scoop or spoon, fill every other muffin liner with batter. The liners should be filled to just below the top
  12. Bake for 8 minutes at 400 degrees F then reduce the oven temperature to 350 degrees F. Bake for an additional 13-15 minutes
  13. The muffins are done when slightly golden on top and edges. A toothpick should also come out of the center clean
  14. Let cool for 10 minutes in the pan
  15. Enjoy!
Granulated sugar and lemon zest in a large mixing bowl.
Granulated sugar and lemon zest
Rub the zest into the sugar using your fingers to release the oils
Eggs and vanilla added to sugar.
Add the eggs, vanilla and butter
Mixing wet ingredients in the bowl.
Whisk until combined then add the salted butter, milk, lemon juice
Mixing wet ingredients in the bowl.
And the greek yogurt
Mixing wet ingredients and poppy seeds in the bowl.
Mix until combined then add the poppy seeds
Mixing wet ingredients and poppy seeds in the bowl.
Mix until evenly distributed
Mixing wet and dry ingredients together in the bowl.
Add the dry ingredients
Lemon poppy batter resting in the bowl.
Fold into the batter until just combined
Lemon poppy batter in the muffin liners.
Rest the batter then transfer to the muffin tin
Baked lemon poppy muffins in a muffin tin.
Bake and enjoy!

Key factors to making these muffins perfect

  1. Prepping Your Muffin Tin – make sure you line your muffin tins with muffin liners. You can also spray with nonstick but muffin liners make the removal process easier.
  2. 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.
  3. Lemon Juice and Zest – Some recipes only call for lemon zest or juice, however, I prefer to use both. It creates the perfect punch of lemon flavor in every bite!
Lemon Poppy Seed Muffin on a plate.

Frequently Asked Questions

Can I use regular all purpose flour instead of gluten-free flour?

Yes! The regular all purpose flour will give you the same result and you can substitute at a 1:1 ratio.

What is the best milk to use?

I use whole milk but you can also use any milk you prefer. The only milk I don’t recommend using is coconut milk. That could change the texture and would be a strong flavor to add.

Can I add mix-ins to the batter?

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.

What can I do to make my muffins rise higher?

First, resting the batter! It allows the starches in the flour to absorb the moisture, resulting in a more stable batter.

Another tip is to add a muffin liner in every other muffin mold. This gives the muffin enough space to rise freely and create the ideal dome top.

How should these muffins be stored?

Store in an airtight container for up to 5 days at room temperature (or in the fridge) or in the freezer for up to 1 month.

Lemon Poppy Muffin with a bite taken out on a cooling rack.
Lemon Poppy Muffin with a bite taken out.
5 stars (4 ratings)

Gluten-Free Lemon Poppy Seed Muffins

Prep Time: 15 minutes
Cook Time: 22 minutes
Total Time: 37 minutes
Yield: 12 muffins
Gluten-Free Lemon Poppy Seed Muffins are fluffy, bright and full of delicious flavor. Using simple ingredients they are easy to make and a perfect way to start your day.
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Ingredients
 

  • 1/2 cup salted butter, melted and cooled
  • 2 large eggs
  • 3/4 cup granulated sugar
  • 1/2 cup whole milk
  • 1/4 cup greek yogurt, 2% or 5%
  • 1 lemon, both juice and zest
  • 1 tsp vanilla extract
  • 1 3/4 cup gluten free all purpose flour
  • 1 tbsp baking powder
  • 1/2 tsp baking soda
  • 2 tbsp poppy seeds

Instructions
 

  • Preheat the oven to 400 degrees F
  • Add the granulated sugar and lemon zest to a large mixing bowl
  • Rub the zest into the sugar to release the oils using your fingers
  • Add the butter, eggs, milk, greek yogurt and vanilla extract
  • Whisk until combined
  • Add in the lemon juice and poppy seeds
  • Mix until fully combined
  • Fold in the flour, baking powder and baking soda
  • Mix until just combined
  • Let the batter rest for 30 minutes to 1 hour
  • Using a 2 tbsp cookie scoop or spoon, fill every other muffin liner with batter. The liners should be filled to just below the top
  • Bake for 8 minutes at 400 degrees F then reduce the oven temperature to 350 degrees F. Bake for an additional 13-15 minutes
  • The muffins are done when slightly golden on top and edges. A toothpick should also come out of the center clean
  • Let cool for 10 minutes in the pan
  • Enjoy!

Nutrition

Serving: 1muffin, Calories: 206kcal, Carbohydrates: 27g, Protein: 4g, Fat: 10g, Saturated Fat: 5g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 3g, Trans Fat: 0.3g, Cholesterol: 53mg, Sodium: 230mg, Potassium: 59mg, Fiber: 2g, Sugar: 14g, Vitamin A: 300IU, Vitamin C: 5mg, Calcium: 119mg, Iron: 1mg
Author: Jessica Selensky
Course: baked good, Breakfast, brunch, Snack
Cuisine: American
Keywords: breakfast muffins, gluten free muffins, gluten free recipes, gluten-free baking, lemon, lemon muffins, lemon poppy seed 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!