Paleo Lemon Poppy Seed Cookies

Remember when I brought you those fabulous lovely lemon cookies a couple of years back? If you tried them, you know how good they were.

After I first published those cookies, I wanted to make you another cookie that just about anyone could enjoy so I combined my lemon cookies and almond flour sugar cookies into one glorious lemon-flavored sugar cookie packed with poppy seeds and topped with a sweet, zesty lemon glaze. GUYS, these paleo-friendly, gluten free lemon cookies are sooooo soft and chewy!

What more could you want? I mean, besides a cold glass of your favorite milk to pair with them. Or maybe even an afternoon latte?

Mmmm now we’re talkin’. Clearly, my favorite 3pm snack = cookies and coffee.

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ingredients for paleo lemon poppy seed cookies on a grey board

What you’ll need to make the best gluten free lemon cookies

These delicious paleo lemon poppy seed cookies are made with a mix of almond & coconut flour and are bursting with delicious lemon flavor. Don’t forget that bright glaze! Here’s everything you’ll need to make them:

  • Almond flour: these cookies call for blanched almond flour. There is no substitute in this recipe.
  • Coconut flour: I like to use coconut flour in my paleo recipes, but if you aren’t paleo, gluten free oat flour is a good substitute most of the time.
  • Baking soda: you’ll just need a pinch for this recipe.
  • Coconut oil: I prefer to use virgin coconut oil in this recipe because it adds flavor, but melted butter or melted vegan butter is a great option!
  • Sugar: granulated or organic cane sugar is best in this recipe. You can use coconut sugar, too, which is paleo-friendly. Note that it will change the color of the cookies to a golden brown hue and the flavor may slightly change a bit, but it will still be delightful.
  • Egg: you’ll need one egg, and it’s best if the egg is at room temperature before you bake with it. These cookies work very well with a ‘flax egg’ if you want to make them vegan. More vegan notes can be found in the recipe note section!
  • Fresh lemon zest and juice: for that true, fresh lemon flavor.
  • Almond extract: a hint of almond extract (not vanilla extract!) brings out the incredible flavor in these lemon poppy seed cookies. Don’t skip it.
  • Poppy seeds: You don’t need to include poppy seeds in this recipe, but I’m addicted to the flavor and texture it gives the cookies.

How to keep them paleo-friendly

If you’re looking for true paleo lemon cookies, feel free to use coconut sugar in the recipe and my paleo powdered sugar in the glaze. Easy!

gluten free lemon cookies on a baking tray next to a bunch of flowers

How to make vegan lemon cookies

If you want to make these lemon poppy seed cookies vegan, simply use a ‘flax egg’ instead of a regular egg in the recipe (1 tablespoon flaxseed meal + 3 tablespoons water). I’ve tested them and they worked perfectly!

Can I use a different flour?

I would not recommend substituting the almond flour in this recipe as the texture will greatly change. However, you can try substituting the coconut flour for a gluten free oat flour if you’d like. Learn how to make your own oat flour here!

Looking to use regular, all purpose flour? Try these lemon cookies instead!

healthy lemon cookies with glaze on a baking sheet

Tips for the best gluten free lemon cookies

The best part about these healthy lemon cookies? They’re easy to make right in one bowl! Here are some tips for making them:

  • Don’t skip the parchment paper. To make sure the cookies don’t stick to the pan, use parchment paper on your baking sheet.
  • Pack your almond flour. Be sure to pack the almond flour as you would with brown sugar. Do not pack the coconut flour.
  • Use a room temperature egg. Simply run your egg under warm water for a minute before using it in the recipe.
  • Fresh lemon juice is best. Make sure you use freshly squeezed lemon juice for this recipe. Do not use lemon concentrate, it’s too potent and sour.
  • Don’t forget the lemon zest. The lemon zest is very important to flavoring these lemon poppyseed cookies. Here’s the inexpensive zester I recommend.
  • Allow cookies to cool. Before you ice these cookies, make sure to let them cool completely on a cooling rack so that the icing doesn’t soak into the cookie. If you are in a rush and want to speed up the process you can put the cookie sheet in the freezer for 10-15 minutes after baking.

Storing & freezing tips

  1. To store: Simply store these healthy lemon poppy seed cookies in an airtight container at room temp for up to 5 days.
  2. Freeze the dough. Simply roll your grain free lemon cookies into dough balls and place them on a cookie sheet lined with parchment paper. Chill the dough in the freezer for 30 minutes. Once the cookie dough balls firm up, transfer them to a reusable freezer-safe bag or container for up to 3 months. When ready to bake, simply bake the cookies as directed. You’ll likely just need to add a few extra minutes of baking time!
  3. Freeze baked cookies. Wait for the cookies to cool completely, then transfer them to a reusable freezer-safe bag or container lined with wax or parchment paper. I like to place them in a single layer to avoid any cookies breaking. Cookies will keep well for up to 2 months. Once ready to eat, simply thaw out at room temperature, add the glaze and enjoy.

grain free lemon cookies with glaze on a baking sheet

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I hope you love these easy paleo lemon poppy seed cookies! If you make them be sure to leave a comment and rate the recipe below. I’d love to hear from you and it helps encourage others to make the recipe too! Thank you — xo!

Paleo Lemon Poppy Seed Cookies

4.98 from 38 votes

Prep Time 10 minutes

Cook Time 10 minutes

Total Time 20 minutes

Gorgeous paleo lemon poppy seed cookies made with a mix of nutritious coconut flour and almond flour then topped with an easy, sweet & zesty lemon glaze. These grain and gluten free lemon cookies are the perfect healthy spring treat that’s dairy free and easily vegan!


  • For the wet ingredients:
  • 1/4 cup melted and cooled coconut oil (or sub melted butter or vegan butter)
  • 1/3 cup organic cane sugar (or sub coconut sugar)
  • 1 egg, at room temperature
  • 1/2 tablespoon fresh lemon juice
  • 1/4 teaspoon almond extract⠀
  • zest from 1 large lemon (about 1 tablespoon lemon zest)
  • For the dry ingredients:
  • 1 cup packed fine blanched almond flour
  • 2 tablespoons coconut flour
  • 1 tablespoon poppyseeds
  • 1/4 teaspoon baking soda⠀
  • 1/4 teaspoon salt
  • Optional for rolling the cookies:
  • 1/4 cup granulated sugar
  • For the lemon glaze:
  • 1/2 cup powdered sugar⠀
  • 1 tablespoon fresh lemon juice, plus more if necessary to thin
  • 1 teaspoon lemon zest


  1. Preheat oven to 350 degrees F. Line a baking sheet with parchment paper.

  2. In a large bowl, mix together the wet ingredients: melted and cooled coconut oil, sugar, egg, fresh lemon juice, almond extract & lemon zest. Mix until smooth and combined.

  3. Add in the almond flour, coconut flour, poppyseeds, baking soda and salt. Stir to combine. Let dough sit for 5 minutes. Roll into 12 balls. If you want you can roll each ball in a bit of sugar. Place cookie dough balls 2 inches apart on baking sheet. Gently flatten slightly with your hand. Bake for 10-12 minutes. Let cool completely on baking sheet.

  4. Make the glaze by mixing together the powdered sugar, fresh lemon juice and lemon zest until smooth. place about a 1/2 tablespoon over each cookie. Enjoy! Makes 12 cookies

Recipe Notes

To make vegan: simply use a ‘flax egg’ instead of a regular egg in the recipe (1 tablespoon flaxseed meal + 3 tablespoons water).

To keep paleo: you can use coconut sugar (more paleo-friendly), but just know that it will change the color of the cookies to a golden brown hue and the flavor may slightly change a bit.

If you want to skip the frosting, you can, but I think it makes these cookies AMAZING and full of lemon flavor.

See the full post for storing & freezing tips.


Servings: 12 cookies

Serving size: 1 cookie

Calories: 147kcal

Fat: 10g

Saturated fat: 4.4g

Carbohydrates: 13.6g

Fiber: 1.6g

Sugar: 10.8g

Protein: 2.8g

Recipe by: Monique Volz // Ambitious Kitchen | Photography by: Eat Love Eats

This post was originally published on April 17th, 2019, republished on March 9th, 2021, and republished on April 23rd, 2023.