These Gluten-Free Vegan Lemon Poppy Seed Muffins are light, fluffy, and bursting with fresh lemon flavor. Whether you're baking them for brunch, a quick snack, or just to brighten up your afternoon with a cup of tea or my Refreshing Ginger Pink Lemonade, these vegan muffins deliver that perfect balance of tart, sweet, and satisfying.
Lemon poppy seed anything takes me right back to warm spring or summer mornings, coffee in hand, and a fresh batch of muffins on the table. You can't even tell that they're vegan and refined sugar-free because they hit all the right notes. Best of all, they're also super easy to make. Think fluffy texture, zippy citrus flavor, and that tiny crunch of poppy seeds in every bite, similar to my Lemon Poppy Seed Overnight Oats—another great breakfast or dessert. I tested this recipe with different plant milks, and soy milk gave me the best texture, but feel free to experiment! Let's make them together.
As an Amazon Associate, I earn from qualifying purchases.
This recipe features several affiliate links, meaning I will earn a small commission if you purchase through these links.
Jump to:
Ingredients To Make Vegan Lemon Muffins:
Here's what you need to make these vegan lemon muffins. You probably have most of the ingredients already in your pantry.
- Gluten-Free Flour Blend: I'm using a blend of oat flour and gluten-free flour. It's a great combo for that soft crumb without needing all-purpose flour. I've tested this so many times, like with my Easy Bakery Style Pistachio Muffins, and I find it gives the perfect texture. Make sure you use gluten-free oat flour.
- Leavening Agents: I'm using both baking soda and baking powder to give the batter the lift it needs for fluffy muffins with a nice rise.
- Maple Crystals: It's my favorite healthy sweetener, and I use it a lot, like in my Vegan Dubai Chocolate Brownies or Creamy Hazelnut Steel-Cut Oats, to name a few. This beautiful, unrefined sweetener offers a rich caramel-like depth. With their warm maple flavor, Wilderness Poets Maple Crystals elevate any healthy baked good while keeping the recipe refined sugar-free, fully plant-based, and still adding nourishing vitamins and minerals.
- Poppy Seeds: They add that irresistible crunch and a classic touch to lemon baked goods. Use leftovers to make my Lemon Poppy Seed Baked Oats.
- Ground Flaxseed: Ground flaxseeds mixed with water create a gel-like “flax egg” that acts as a vegan-friendly binder in these vegan lemon poppyseed muffins—no eggs needed. Just let the mixture sit for 5–10 minutes in a large mixing bowl to thicken up. It also adds a boost of fiber!
- Fresh Lemon Zest + Fresh Lemon Juice: Double the citrus flavor. Meyer lemons work beautifully here for a slightly sweeter zing.
- Vanilla Extract: It deepens the flavor of the muffin batter while adding a layer of complexity that pairs well with the zesty flavors of the lemon.
- Vegan Sour Cream or Yogurt: Helps keep the center of the muffin moist and tender.
- Applesauce: A great way to add moisture without needing melted coconut oil or vegetable oil in baked goods.
- Non-Dairy Milk: Soy milk gives the best structure here and creates moist muffins with the perfect soft crumb.
See the recipe card for quantities.
How To Make Them:
You’ll only need one large bowl, one muffin tin, and a little bit of patience while they cool! Here's what to do.
- Make Flax Eggs: In a large mixing bowl, mix ground flaxseed with water. Let it sit until you get a gel-like consistency.
- Add Dry Ingredients: Once gelled, stir in all the dry ingredients until well combined.
- Add Wet Ingredients: Add all the wet ingredients. Mix gently until just combined—don’t overmix.
- Bake & Cool: Scoop the batter into muffin cups until ¾ full, then bake until a toothpick comes out clean or with a few moist crumbs. Cool the muffins in the muffin tin for 5 minutes, then transfer to a cooling rack.
- Make the Maple Glaze: Whisk melted coconut with maple syrup until smooth. Drizzle over cooled muffins. for that glossy finish.
Top Tips:
Here are a few of my tips to make the best gluten-free vegan lemon poppy seed muffins.
- Room Temperature: It's best to use room-temperature ingredients for better blending, and it creates a more even bake.
- Cupcake or Muffin Liners: Use muffin molds or muffin liners to prevent sticking if you’re not using a non-stick muffin pan.
- Don't Overbake: Avoid overbaking to maintain moist muffins.
- For Extra Lemon Flavor: I always prefer fresh lemon juice and lemon zest in all my lemony baked goods, like, for example, my Raw Vegan Lemon Raspberry Bars, but you can add a few drops of lemon extract to your batter for a more intense lemon flavor.
Variations And Substitutions:
Here are a few suggestions of swaps or variations that can work in case you don't have something on hand or want to change things up.
- Yogurt Alternative: You can also try cashew milk yogurt for extra creaminess if you don't have a vegan sour cream.
- Soy Milk Alternative: Soy milk does, in my opinion, give you the best results in terms of texture, but oat milk, almond milk, or even cashew milk will also work well.
- Add Blueberries: It pairs well with the citrusy flavors similar to my Gluten-Free Vegan Lemon Blueberry Muffins.
- Sweetener: You can swap maple crystals for coconut sugar or organic cane sugar if needed. But I highly recommend trying out the maple crystals, especially if you plan to make some of my other vegan goodies on the blog.
Storage:
Store in an airtight container at room temperature for up to 3 days. To keep longer, place in a freezer bag and freeze for up to 2 months. Let thaw at room temperature before eating, or warm slightly in the oven to enjoy that fresh-baked taste again.
Equipment Needed:
- Large Mixing Bowl: To make the muffin batter and flax eggs.
- Muffin Tin or Muffin Pan: To bake the lemon poppy seed muffins.
- Measuring Cups: To get the exact ingredients.
- Muffin or Cupcake Liners: To line the muffin pan.
- Ice Cream Scoop or Spoon: To scoop batter into the muffin pan.
- Cooling Rack: To cool the muffins.
- Small Bowl: To make the coconut-maple glaze.
Recipe FAQs:
You can, but it will no longer be gluten-free. Be sure to reduce the moisture slightly to adjust.
Soy milk or almond milk typically gives the best texture, but oat milk works if that's all you have on hand.
Yes! Just skip them or replace them with chia seeds for a similar texture.
Yes—but highly recommended! It’s a simple maple glaze that makes these muffins bakery-worthy.
More Favorite Muffin Recipes To Try Next:
Looking for more vegan muffins to bake at home? Make sure to check out some of the other recipes on my website!
These gluten-free vegan lemon poppyseed muffins are easy to make, totally customizable, and perfect for breakfast, snacks, or sharing with friends. Happy baking!
If you try this Gluten-Free Vegan Lemon Poppy Seed Muffins Recipe, I’d really love to hear your thoughts in the comments below. I’d also really appreciate a recipe card rating! Thank you for supporting The All Natural Vegan!
Gluten-Free Vegan Lemon Poppy Seed Muffins
Equipment
Ingredients
Dry Ingredients:
- 2 cups oat flour
- 1 cup gluten-free flour
- 1 cup maple crystals
- 1 teaspoon baking soda
- 1 ½ teaspoons baking powder
- 1 tablespoon poppy seeds
- 2 tablespoons ground flaxseed
- 1 tablespoon lemon zest
Wet Ingredients:
- ¼ cup vegan sour cream or yogurt
- 1 cup fresh lemon juice
- 2 teaspoons vanilla extract
- ¼ cup plant-based milk I recommend unsweetened soy milk for best results
- ½ cup unsweetened applesauce
- 6 tablespoons water
Glaze Ingredients:
- 3 tablespoons coconut butter warm it up for best results
- 4 tablespoons maple syrup
Instructions
Preheat oven + prepare pan:
- Preheat your oven to 350°F (175°C).
- Line a muffin tin with paper or parchment liners.
Make flax egg directly in a mixing bowl:
- In a large mixing bowl, add 2 tablespoon ground flaxseed + 6 tablespoon water.
- Let it sit for about 5–10 minutes to gel.
Add dry ingredients:
- Once the flax egg is set, add the oat flour, gluten-free flour, maple crystals, baking soda, baking powder, poppy seeds, and lemon zest to a large bowl.
- Whisk or stir to evenly combine.
- Add wet ingredients directly to the bowl:
- Add the vegan sour cream, lemon juice, flax egg, vanilla, plant-based milk, and applesauce right into the bowl with the dry mixture.
- Mix until just combined — avoid overmixing.
Scoop & bake:
- Spoon batter into the muffin tin, filling each about ¾ full.
- Bake for 30 minutes or until a toothpick comes out clean or with a few moist crumbs.
Cool completely:
- Allow the muffins to cool in the pan for 5 minutes, then transfer to a wire rack.
Make the glaze:
- Stir together melted coconut butter and maple syrup until smooth.
- Drizzle over cooled muffins.
More Vegan Lemon Recipes:
Are you a fellow lover of all things lemon? Check out some of these recipes!
Shilpa
These muffins are so good! Perfect taste, texture and healthy. We loved it.
nancy
wow these muffins are so freakishly good! i love the lemon and how moist it is
Michelle
Love this veganized classic!! The fresh zest makes it a true showstopper and gives that extra special tough you don't get with the store-bought kind.
dave
super tasty and pinned to make again~