Gluten-Free Lemon Poppy Seed Muffins (Paleo)

Name: Gluten-Free Lemon Poppy Seed Muffins (Paleo)
Prep time: 10 min
Cook time: 25 min
Total time: 35 min
Ingredients: 3/4 cup cassava flour; 1 tbsp poppy seeds; 1/2 tsp baking powder (make sure it is gluten free and uses cornstarch or arrowroot starch instead of wheat starch as the base); 1/4 tsp baking soda; 1/8 tsp sea salt; 1/4 cup maple syrup; 1/4 cup coconut oil (melted and cooled); 1/4 cup full fat coconut milk; 2 tbsp lemon juice; 1 large egg; 1 tbsp lemon zest; 1/2 tsp pure vanilla extract; 2 tbsp coconut butter; 1 tbsp raw honey; 1 tbsp lemon juice; 1 tbsp coconut milk; 1 tsp lemon zest (plus more for garnish)

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These gluten-free lemon poppy seed muffins are bright, zesty, and bursting with fresh lemon flavor. Made with cassava flour, naturally sweetened, and topped with a simple lemon glaze, they’re the perfect on-the-go breakfast or snack! Especially paired with a cup of coffee.

Why You’ll Love These Lemon Poppy Seed Muffins

My mood has been at an all time high recently now that the weather is finally warming up, the days are crazy long and it really feels like spring. With that, I’m looking forward to all the lighter and more colorful dishes, along with some grill recipes, and tart baked goods like orange cookies with creamsicle frosting and pomegranate orange scones to celebrate this new season.

Enter these lemon poppy seed muffins! They’re completely grain-free and nut-free, made with cassava flour for the perfect fluffy muffins, and loaded with a bright lemon flavor that makes them taste so spring-y. I’ve been starting my mornings with one of these beauties and a hot mug of coffee, and let me tell you, it’s been the best little mood booster to kick off my day.

While these homemade lemon muffins are amazing on their own, the coconut lemon glaze takes them to a whole new level. It adds extra moisture, a touch of sweetness, and an even bigger punch of fresh lemon flavor. Also, don’t forget the poppy seeds. They add a nutty and slightly fruity flavor that compliments the lemons and makes the muffins extra tasty and special! Basically, these muffins are spring in baked form, and if you’re as obsessed with lemony treats as I am, you need to make them ASAP.

Ingredient Notes

Here are a few notes on the key ingredients for these gluten-free lemon poppy seed muffins! Jump to the recipe card for the full recipe and exact measurements.

Cassava flour: A grain-free, gluten-free alternative that gives these muffins a soft, fluffy texture. Almond flour or a blend of almond and tapioca flour can work as a substitute, but the texture may change slightly.
Poppy seeds: Add a subtle crunch and a nutty flavor that pairs beautifully with bright citrus flavor. Chia seeds can be a swap if needed, though they’ll absorb more moisture.
Baking powder & baking soda: The combination of these two gives the muffins a nice rise and keeps them from getting too dense.
Maple syrup: A natural sweetener that keeps these muffins moist while adding a rich, caramel-like depth. Honey or coconut sugar (with a slight texture adjustment) can be used instead.
Coconut oil: Provides moisture and richness without overpowering the lemon flavor. Avocado oil or melted butter (if not dairy-free) are great alternatives.
Full-fat coconut milk: Adds creaminess and tenderness. If you prefer, you can swap in greek yogurt or sour cream for an extra boost of moisture.
Lemon juice & lemon zest: The stars of the show! They bring that bright lemon flavor, and if you want an even stronger citrus kick, you can add a dash of lemon extract.

Coconut Lemon Glaze

Coconut butter: Makes the glaze thick, creamy, and slightly sweet. Cashew butter can work, but the coconut flavor will be less pronounced.
Raw honey: Naturally sweetens the glaze. Maple syrup can be swapped in, though the consistency will be a bit thinner.
Lemon juice & lemon zest: Adds brightness and balances the sweetness, bringing out that tangy lemon flavor. Lemon zest is an optional final touch but I highly recommend it!
Coconut milk: Helps smooth out the glaze while keeping it dairy-free. Any plant-based milk can work, but full-fat versions make for the creamiest result.

How to Make Gluten-Free Lemon Poppy Seed Muffins

Step 1: Preheat the oven to 350 degrees F.

Step 2: Line a 6-cup muffin tin with a muffin liner (muffin cups), or grease with coconut oil.

Step 3: In a large bowl, combine cassava flour, poppy seeds, baking powder, baking soda, and sea salt, and mix well.

Step 4: In a separate bowl, combine maple syrup, coconut oil, coconut milk, lemon juice, egg, lemon zest, and vanilla extract. Whisk together.

Step 5: Pour wet ingredients into dry ingredients and stir together until just combined.

Step 6: Divide the muffin batter into the muffin pan, filling each cup about 2/3 of the way up.

Step 7: Bake for 20-25 minutes, or until a toothpick inserted at the center of a muffin comes out clean.

Step 8: Let muffins cool in the tin for 5 minutes before transferring to a wire rack.

Coconut Lemon Glaze

Step 1: In a small saucepan, combine all ingredients and heat over low heat until fully melted and combined.

Step 2: Drizzle on top of the muffins. If you want, add more lemon zest on top of the glaze.

Step 3: Let it cool. The glaze will harden once fully cooled.

Expert Tips

Don’t overmix the batter. Stir just until combined for the best results!
Use fresh lemon juice and zest. It makes all the difference in flavor. Bottled juice just isn’t the same. Also, the lemon juice in this recipe isn’t just for flavor – it reacts with the baking soda to help create light and fluffy muffins, so don’t skip it!
Let the muffins cool before glazing. If they’re too warm, the glaze will melt right off instead of setting beautifully on top.
If your batter feels too thick, a splash of additional coconut milk or a spoonful of greek yogurt can help loosen it up.
Always check that your baking soda and baking powder are fresh – expired leaveners won’t give you that perfect lift!

Serving Tips

These muffins are best enjoyed slightly warm with a cup of coffee, tea, matcha, or even dairy free hot chocolate.

Storage Tips

Store in an airtight container for up to 2 days. Or keep in the fridge (also in an airtight container) for up to 5 days. Reheat in the microwave for 10-15 seconds.

Wrap individually in plastic wrap and store in an airtight container for up to 3 months. Let them thaw at room temperature or warm them in the oven before serving.

Recipe FAQs

Can I make these muffins egg-free?

You can substitute the egg with a flax egg (1 tbsp ground flaxseed + 3 tbsp water). The texture will be slightly different, but I’m sure it will still be delicious!

Can I use a different flour?

Cassava flour works best for this recipe, but a mix of almond and tapioca flour can work in a pinch. If using purpose flour, you’ll need to adjust the liquid ingredients slightly.

Do I need xanthan gum for this recipe?

Nope! Unlike many gluten-free baking recipes that require xanthan gum, these muffins hold together perfectly thanks to the combination of cassava flour and eggs.

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