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Lemon Poppy Seed Muffins (Paleo + No Refined Sugar)

These bakery-style Lemon Poppy Seed Muffins are fluffy, tangy and so simple to prepare.

Lemon Poppy Seed Muffins are one of our favorite combinations. There’s something about a sweet, yet slightly tangy flavor combined with crunchy poppy seeds that’s downright addicting. The batter in this recipe is made with simple ingredients, contains no refined sugar, is gluten free and is Paleo friendly.

What makes these muffins so amazing? The freshly grated lemon zest, lemon juice, almond flour and honey create a fluffy, lightly sweetened muffin that’s bursting with flavor. These muffins are delicious as is or with a sweet, yet tangy glaze.

If you’re looking for a refreshing breakfast, afternoon snack or delicious dessert, you’ll want to give this one a try. You’ll be hooked after just one bite!

How to make homemade powdered sugar for the lemon glaze

If you enjoy a slightly sweeter muffin, you can top your muffins with a delicious lemon glaze. All you need is a little powdered sugar, lemon juice and coconut oil. Because most powdered sugar is made with super refined white sugar and then mixed with cornstarch to prevent caking, we wanted to share a more FfL-friendly, real food Powdered Sugar recipe.

This simple Powdered Sugar (Confectioners’ sugar) recipe is made in 30 seconds, using only two ingredients and a high-speed blender (or food processor).

Kid-friendly and great for school lunches

Lemon Poppy Seed Muffins are great for school lunches. If frozen, pull a muffin out in the morning, put it in your kiddo’s lunchbox and it will be thawed by the time they’re ready to eat!

How to store and freeze your muffins

Storing: Store your unglazed muffins at room temperature for up to 4 days. If glazed, store them in the refrigerator. You can reheat them in the microwave before eating them, pop them in the toaster oven or enjoy them at room temperature. We typically keep our muffins in the fridge and warm them in the toaster oven on low for 2-3 minutes before eating them.

Freezing: To freeze these muffins, let them cool completely. Place unglazed muffins in an airtight container or remove excess air and store them in a Ziploc baggie. These muffins should last for up to 3 months in the freezer. Let them defrost overnight in the refrigerator or at room temperature before eating.

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Lemon Poppy Seed Muffins (Paleo + No Refined Sugar)

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Lemon Poppy Seed Muffins:

Lemon Glaze: (optional)

  • 1/4 cup powdered sugar (recipe linked above)
  • 2 teaspoons lemon juice (about 1/4 lemon)
  • 1 teaspoon virgin coconut oil, melted


  1. Preheat oven to 325 degrees. Grease a muffin tray with coconut oil or line with cupcake liners. Set aside.
  2. In a medium mixing bowl, combine dry ingredients (almond flour, coconut flour, poppy seeds and baking soda).
  3. In a large mixing bowl, mix honey and melted coconut oil. Add remaining wet ingredients (1/3 cup lemon juice, zest from 2 lemons, eggs and vanilla).
  4. Pour the dry ingredients into the wet. Fold ingredients together until just combined, being careful not to overmix. Spoon the batter evenly into each cup or liner, filling all the way to the top.
  5. Bake for 15-18 minutes or until a toothpick inserted in the center comes out clean. Allow muffins to cool for 5 minutes in the muffin pan, then transfer to a wire rack to finish cooling.
  6. If you want to glaze your muffins, warm Lemon Glaze ingredients in microwave (about 10 seconds), whisk together until smooth and drizzle over cooled muffins.
  7. Glazed muffins stay fresh stored in the refrigerator for up to 1 week. Unglazed muffins stay fresh stored in an airtight container at room temperature for a few days.


Lemon: 1 medium-sized lemon yields approximately 1 tablespoon of lemon zest and 2-3 tablespoons of juice.

Freezing instructions: For longer storage, freeze muffins in an airtight container for up to 3 months. Allow to thaw in the fridge overnight. Warm in the microwave or toaster oven if desired.

Paleo-friendly: Omit the lemon glaze.

We recommend organic ingredients when feasible.

Always check for FfL-friendly ingredients.

  • Prep Time: 15 min
  • Cook Time: 20 min

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Hi beautiFULL, We’re Pam and Kalie

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