Lemon Poppy Seed Muffins are bursting with fresh lemon flavor and made healthy by using a gluten-free flour, dairy-free coconut oil, and honey as a natural sweetener. This easy and healthy recipe can be enjoyed for breakfast, snack, or even dessert and are a perfect Spring or Easter brunch!

A tray full of healthy, gluten-free lemon muffins with a powdered sugar glaze and poppy seeds.

Lemon Poppy Seed Muffins Recipe

Spring is almost here!!  The bluebonnets are in full bloom, the trees are turning green, and our house has been bursting with batch after batch of these easy and healthy lemon poppy seed muffins.

You think I am kidding?  One thing is certain, testing and tweaking breakfast muffins that are made dairy-free and gluten-free normally results in SO many test batches that I do not know what to do with them.  Luckily I have TONS of friends and family who are more than happy to take one for the team and try out 2 or 3 versions of this easy recipe.

But the best part?  You can rest assure that this healthy breakfast recipe has been through the ringer and is the absolute BEST healthy lemon muffin recipe you will find on the web… and even better than any you would find in the store or your favorite cafe!

Two lemon poppy seed muffins in a stack with a bite taken out of one next to a lemon wedge.

How to Make

Making this breakfast recipe is very much like other muffin recipes you might have tried.  It is a quick and easy process and only requires a few steps.

  1. Preheat oven to 350°F .
  2. Whisk together your wet ingredients (i.e. eggs, milk, oil, etc.)
  3. In a separate bowl, whisk together your dry ingredients (i.e. flour, baking soda, etc.)
  4. Combine your wet and dry ingredients and mix until JUST smooth.
  5. Add fresh lemon zest and poppy seeds into the batter.
  6. Fill tray with muffin cup liners.  Pour enough batter into each cup until it is almost full.
  7. Bake in preheated oven for 24-26 minutes, or until toothpick inserted into the center comes out clean.
  8. Whisk together glaze ingredients and drizzle over cooled muffins.  Enjoy!

The ingredients for a lemon poppy seed muffins recipe.


These lemon poppy seed muffins are made vegetarian, gluten-free, and dairy-free by using a few healthier ingredients:

  • Gluten-free Flour: Bob’s Red Mill 1-to-1 is the gluten-free flour that is used in this recipe and has the best results.  You can also make your own gluten-free flour at home, too.
  • Coconut Oil: Using coconut oil in place of butter makes them extra moist and also dairy-free.
  • Almond Milk: In order to keep this recipe completely dairy-free, almond milk is used in place of regular milk.
  • Honey: Instead of using your typical processed white sugar, local honey is used.
  • Eggs: Pasture-raised organic large eggs help give them their fluffy texture.
  • Baking soda, vanilla, fresh lemon juice and zest, and poppy seeds.

Lemon zest and poppy seeds in a healthy lemon muffin batter.


While following this lemon poppy seed muffin recipe exactly is highly recommended, there are a few ingredient swaps and variations you can try without too much sacrifice on taste or texture.  A few variations include:

  • Regular all purpose flour can be used in place of the gluten-free flour.
  • Butter can be substituted for the coconut oil if not dairy-free.
  • Honey can be replaced with agave nectar or maple syrup.
  • Soy milk, cashew milk, or regular milk can be used instead of the almond milk.
  • You can try to substitute flax eggs for the regular eggs to make these vegan, although I have not personally tested this variation.

Powdered sugar, milk, and lemon zest being whisked together to make a muffin glaze.

Easy Lemon Glaze

If you want to leave off the lemon glaze on this muffin recipe, you have my FULL permission.  They will still taste incredible and will be completely refined sugar-free.

However, if you are down to splurge just a bit, this lemon glaze is DA BOMB and takes this recipe over the top.

And it is SO flipping easy to make.  I mean seriously.

You will only need powdered sugar, a touch of milk, and lemon zest.

Voila!!  The perfect glaze to fancy up this lemon poppy seed muffin recipe.

Eggs, coconut oil, and honey being whisked together to show how to make lemon poppy seed muffins.

Pro Tips and Tricks

  • Let the eggs and milk sit at room temperature at least 30 minutes before preparing your muffin batter.  You do not want them to be cold.
  • Do NOT over mix the batter.  This will result in a dense, not fluffy texture.
  • Spray your muffin liners thoroughly with non-stick cooking spray to prevent sticking to the liners.
  • While this recipe is the absolute BEST when enjoyed within 24-48 hours of baking, there are a few things you can do to extend their shelf life:
    • Refrigerate the muffins between servings to make them last for 3-4 days.
    • Pop these bad boys in the microwave for 20-30 seconds before enjoying.
    • Slather on a touch of butter (if not dairy-free!) and toast ’em up in the toaster oven.
  • Make sure the coconut oil is COMPLETELY melted.  If it is not, the batter will come out too thick.

Lemon Poppy Seed Muffins with a lemon glaze on a white table.

Can You Freeze Them?

Yes!  You absolutely can freeze them as well as most healthy breakfast muffins.

The best way to freeze leftover muffins is to wrap each one individually in wax paper, tape them closed, and then place in a large freezer-safe ziplock bag.

Muffins will keep well for 3-4 months in the freezer.  When ready to eat, thaw in the refrigerator and reheat in the microwave, oven, or toaster oven.

A navy blue plate full of eight gluten-free lemon poppy seed muffins and a hand grabbing one of them.

Other Breakfast Recipes:

You might also enjoy a little more lemon flavor in this Lemon Creme Brulee!

Tap stars to rate!

4.03 from 40 votes

Lemon Poppy Seed Muffins

Lemon Poppy Seed Muffins are bursting with fresh lemon flavor and made healthy by using a gluten-free flour, dairy-free coconut oil, and honey as a natural sweetener.
Yield 12 muffins
Prep 15 minutes
Cook 25 minutes
Total 40 minutes
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  • cup coconut oil melted
  • 3 eggs large, room temperature
  • cup honey*
  • ¼ cup lemon juice
  • ½ cup almond milk* room temperature
  • 1 tsp. vanilla extract
  • 2 ¼ cups flour* gluten-free 1-to-1
  • 1 tsp. baking soda
  • 2 Tbsp. lemon zest
  • 1 Tbsp. poppy seeds

Lemon Glaze (optional)

  • ½ cup powdered sugar
  • 1 Tbsp. Milk
  • 1 tsp. Lemon zest


  • Preheat oven to 350 degrees.
  • In a medium-sized bowl whisk together coconut oil, eggs, honey, lemon juice, milk, and vanilla.
  • In a separate large bowl combine flour and baking soda. Whisk to combine.
  • Add dry ingredients to wet ingredients and stir until just combined.
  • Add lemon zest and poppy seeds and mix well.
  • Spray non-stick cooking spray into 12 cupcake liners in a muffin pan. Pour 1/3 cup batter into each liner.
  • Bake muffins for 24-26 minutes, or until a toothpick inserted in the center comes out clean.
  • While muffins are baking, whisk together powdered sugar, milk, and lemon zest until smooth. Let muffins cool to room temperature and then drizzle glaze over muffins.
  • Enjoy muffins immediately or store muffins in an airtight container for up to 2-3 days.
Last step! If you make this, please leave a review letting us know how it was!

Tap stars to rate!

4.03 from 40 votes


  • Regular all-purpose flour can be used in place of the gluten-free 1-to-1 blend.
  • Butter or vegan butter may be used in place of coconut oil.
  • Maple syrup or agave nectar can be substituted for the honey.


Calories: 283kcal, Carbohydrates: 38g, Protein: 4g, Fat: 14g, Saturated Fat: 10g, Cholesterol: 40mg, Sodium: 144mg, Potassium: 43mg, Fiber: 2g, Sugar: 21g, Vitamin A: 60IU, Vitamin C: 5.8mg, Calcium: 57mg, Iron: 1.2mg

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

Made this recipe?Leave a comment below!
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    1. Hi! Substituting just almond flour will not work cup-for-cup, but if you’re wanting to make it grain-free you can always use a Paleo flour blend instead!

  1. 5 stars
    It’s so hard finding gluten free recipes that my whole family can enjoy, but I made these for my family yesterday morning and everyone loved them! My family had eaten all of them by the time I went for seconds, which never happens when I bake gluten free! I’m going to make them again today or tomorrow, and was wondering if I made a double batch if I could freeze some of the batter? These are definitely a new family favorite. Thank you!

    1. Yay! So happy to hear you enjoyed the recipe, Sonya! I wouldn’t recommend freezing the batter, but you can bake the muffins and freeze some for later. Thanks so much for taking the time to leave a comment and rating!