Incredibly SOFT and MOIST, these gluten-free lemon poppy seed mini muffins will blow your mind! These muffins have a delicious bright lemony flavor topped with a thin coat of lemon sugar icing.

Celebrate the spring flowers and warm summer weather with moist and flavorful fruit-based desserts. My Gluten-Free Lemon CupcakePeach Cobbler with Biscuits,Lemon Blueberry Buttermilk Cake, and these Gluten Free Carrot Cake Cupcakes are deliciously wonderful ways to use up leftover produce and celebrate the season. Plus, as far as desserts go, these cupcakes are about as healthy as it gets!

One muffin on top of another topped with icing and poppy seeds

Trial and error for the best lemon poppy seed mini muffin recipe

This gluten-free lemon poppy seed muffins recipe comes as a result of a three-year trial. In fact the original recipe was published back in 2017 and looked nothing like this. At one point I gave up on the idea of putting a batch of muffins on the table and hoping no one will notice that they are gluten-free.

Gluten-free baking is hard. Actually, let me re-phrase this… BAKING is hard! I am not a baker by any means, I just love to experiment with it, and I failed more times than I succeeded 🙂 but in the midst of all my trials and errors I was able to make a few recipes work really great, like this gluten-free banana bread that I make all the time, or my gluten-free morning glory muffins and how about those gluten-free apple cider donuts, they are heavenly!!

Muffins in a muffin tray with  fresh lemons, icing and poppy seeds around it

Has it become an easy lemon poppy seed mini muffins experience?

They turned out absolutely perfect! Soft and moist on the inside with a golden crusty top and flavor in every bite. To this recipe I added a top layer of lemon sugar icing for a sweet tangy finish.

It is easier by the time I made another batch. Within two days of reaching the end point on this long trial, I found myself baking these GF lemon poppy seed mini muffins TWICE! My kids absolutely loved these muffins (and no, they could not tell they were gluten-free!), my parents grabbed a few and many of my kids’ friends came by to try my new muffin recipe too! (thanks to Instagram stories, they always see what I’m up to, lol).

I will leave you to the recipe now. Please feel free to email should you have any questions 🙂


More muffins on a chopping board with a bowl of lemons and some sliced ones in the background
Gluten Free lemon poppy seed muffin on top of another topped with icing and some muffins in the background

If you make this easy lemon poppy seed mini muffins, be sure to leave a comment and/or give this recipe a rating! I love to hear from you and always do my best to respond to all your comments. Also, don’t forget to tag me on Instagram for a special shutout and/or a chance of being featured in my newsletter!

Want to save this recipe?
Just enter your email and get it sent to your inbox! Plus you’ll get great new recipes from us every week!
Please enable JavaScript in your browser to complete this form.
Gluten-Free Lemon Poppy Seed Muffins on top of another topped with icing and some muffins and whole lemons in the background

Gluten-Free Lemon Poppy Seed Muffins

by Silvia Dunnirvine
Absolutely DELICIOUS Gluten-Free Lemon Poppy Seed Muffins that are super MOIST soft and flavorful!
Prep: 18 minutes
Cook: 22 minutes
Servings: 18 muffins


  • 2 1/2 cups 1-to-1 gluten-free flour*
  • 3 tbsp poppy seeds, (reserve 1 tbsp)
  • 2 tsp baking powder
  • 1/2 cup sugar
  • 2 whole lemons, zested (reserve the lemons)
  • 2 sticks unsalted butter, softened
  • 3 large eggs or 4 small
  • 1/2 cup milk
  • 6 tbsp lemon juice, about 2-3 lemons
  • 1 1/2 tsp vanilla extract

Sugar Icing

  • 1 cup powdered sugar, sifted
  • 2 tbsp lemon juice


  • Pre-heat oven to 350F degrees. Line 2 muffin pans with paper muffin liners or place 18 silicone muffin cups on a baking sheet.
  • In a stand mixer using the paddle attachment add in dry ingredients along wtih butter softened. That's the flour, baking powder, lemon zest, 2 tbsp poppy seeds and butter. Beat for 2-3 minutes until the crumbles start to stick. You are looking for a stichy sandy consistency here.
  • Add eggs one at a time, then milk, lemon juice and vanila extract as you continue to run the mixer on medium low. Turn mixer to medium high and beat for about 1-2 minutes until mixture is creamy.
  • Using an ice cream scooper fill each muffin cup with muffin batter almost all the way to the top (a little over 3/4 full).
  • Bake for 22-24 minutes in the middle rack position of your oven. Look for a golden top with visible cracks. Transfer to a cooling rack and when ready, top wtih sugar icing and the reserved poppy seeds**

Sugar Icing

  • In a small bowl add in sifted powdered sugar and lemon juice. Using a small whisk in a circular motion stir until fully combined. If the consistency is too thick and sticking to the whisk, add a few drops of lemon juice. Likewise, if its too runny/ liquidy, add a tbsp of sugar.


* It is important to note that not all gluten-free flours are the same. I use Bobs Red Mill 1-to-1 gluten-free baking flour which has the perfect balance of different flour and it already contains xanthan gum, otherwise you will need to add xanthan gum to the recipe. 
** Sugar icing will dry out quickly and poppy seeds will no longer stick. I recommend that you add icing and poppy seeds one at a time.


Calories: 227kcal | Carbohydrates: 27g | Protein: 3g | Fat: 12g | Saturated Fat: 7g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 0.4g | Cholesterol: 59mg | Sodium: 64mg | Potassium: 62mg | Fiber: 1g | Sugar: 13g | Vitamin A: 370IU | Vitamin C: 3mg | Calcium: 67mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Keyword: Gluten-Free Lemon Muffins, Gluten-Free Lemon Poppyseed Muffins, Gluten-Free Muffins
Course: Breakfast, Dessert, Snack
Cuisine: American
Like this? Leave a comment below!
Lemon poppy seed muffins and some more muffins in the background all topped with icing and poppy seeds

Save this recipe to Pinterest for later!

Just hover over the image and click the “Save” button.

Gluten-Free Lemon Poppy Seed Muffins on a chopping board with two muffins placed on a stack. All muffins with icing and poppy seeds.

Hi! I’m Silvia.

My goal is to make cooking simple and enjoyable.

Garden in the Kitchen is full of easy and balanced recipes for busy families. Classics get a healthier twist with additions of veggies or alternative ingredients.

I hope my recipes will inspire you to cook more home meals and above all have fun in the kitchen!

You May Also Like

Leave a comment

Your email address will not be published. Required fields are marked *

Recipe Rating


  1. I love that you made these for yourself and they look so pretty. I can’t remember the last time I made muffins and they are so simple too. I really must make some soon. I think these need some serious sharing!

  2. I was searching for an interesting muffins recipe to make this week for my niece and I came across your recipe. Loved the idea of making lemon flavored cupcakes. Will be making it for sure. 🙂

  3. Lemon and poppy seeds is such a fantastic flavour combination, isn’t it? The texture of these looks amazing. Thanks for sharing!

    1. For sure! It’s definitely one of my favorites because it balances out the sweetness. Thanks so much for stopping by Katerina!

  4. Just made these. They looked and tasted badly. I reread the recipe and see there was no sugar included in the batter. Could that be an omission? I await your reply. Thanks,

    1. Hi Jill, there is a 1/2 cup sugar going into the recipe along with dry ingredients. My apologies that was left out, I have no clue how it was left out. My goodness, so sorry about that!

    1. Hi Laura, I generated a nutritional label for this recipe with all the information, but the calorie count is 227 per muffin