Vegan Lemon Poppy Seed Muffins

NFNut FreeVVegan

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These Lemon Poppyseed Muffins have crispy golden edges and a fluffy, melt-in-your mouth crumb! The perfect breakfast treat. 

I’ve never met a muffin I didn’t like, but these Vegan Lemon Poppy Seed Muffins are truly a treat. They’re packed with flavor and have a light and fluffy interior with crispy golden edges. They’re the perfect breakfast (or anytime) treat!

Three lemon poppy seed muffins on small cooling rack on tiled table


It’s no secret that I love anything lemon poppy seed, but for some reason I haven’t made muffins yet! These muffins are an excellent year-round treat, and they’re easily made vegan with a few simple swaps.

Most muffins are made with yogurt, milk, and eggs – it’s pretty easy to use non-dairy yogurt and milk in place of the first two, but getting the rise from the eggs was the tricky part! After a few tests, I realized the combination of baking soda and ground flax was the answer. The baking soda reacts with the acidic citrus juice to create an initial rise in the oven, while the flax thickens the mixture as it cooks and allows it to set.

Ingredients for muffins on tiled countertop in small bowls. Clockwise text labels read poppy seed, sugar, non-dairy yogurt, salt, baking soda, baking powder, ground flax, non-dairy yogurt, flour, vanilla, and lemon juice and zest

I have made this recipe using both Meyer lemons and “regular” — both work great! Use a regular lemon for a traditional (and more affordable) flavor. Meyer lemons have a slightly floral and herb-y undertones, which adds a different – but still delicious – flavor to these muffins. Vegan lemon muffins if leave poppy seeds out.

Finally, I recommend using soy milk for this recipe – the lemon juice reacts with it to create a vegan buttermilk, which helps make the muffins even fluffier! Soy milk has more natural protein in it so it curdles better, but another non-dairy milk like almond milk or oat milk will work, too.

side-by-side photos of muffin batter in mixing bowl next to muffin tin filled with unbaked batter


These lemon poppyseed muffins come together with only a few simple steps! One final hack I like to do to give these muffins a bakery-style rise and color is to bake them first at a higher temperature, then to reduce the temperature and bake until set. This creates an “oven spring” and allows the muffins to rapidly rise and create classic dome-shaped muffins with crispy golden edges.

  1. Sift the flour and leaveners into a large bowl, then stir in the flax and poppy seeds.
  2. Massage the lemon zest and sugar together in a separate bowl. Stir in the yogurt, milk, oil, lemon juice, and vanilla.
  3. Combine the wet and dry ingredients to form a thick batter.
  4. Divide the batter evenly into a muffin pan, then bake in the oven until golden.

Overhead photo of golden baked muffin tops in baking tin

As an added bonus, your house will smell amazing while the muffins bake in the oven! I like to whip up a quick lemon glaze for the muffins while they bake. It’s an optional add-on, but it adds the perfect tang and sweetness that takes the lemon flavor to a whole new level.

Hand spooning lemon glaze over stack of 3 muffins on small white plate


  • Can I make this recipe gluten-free? I would actually recommend making my Vegan Lemon Poppy Seed Cake instead, which is already GF! You can also try to make this recipe using a gf flour blend, but I haven’t tested it. Let me know if it works for you in the recipe comments below!
  • What is the best way to store muffins? These muffins are delicious straight out of the oven while they’re still warm, and will keep in an airtight container for up to 3 days. Afterwards they will dry out a bit, so I recommend storing them in the refrigerator for up to one week (and reheating in the microwave!), or in the freezer for up to 2 months.
  • To get the best rise on your muffins: first, make sure baking soda and powder are fresh. It’s also important to put the muffins in oven as quickly as possible. The baking soda and lemon juice will react right away once mixed and the batter will begin to rise.

Stack of two muffins with icing dripping down the side of the top one, which is also cut in half

If you’re looking for even more lemon poppy seed recipes, you’ll also love this oatmeal, or these energy bites! Or if you’re craving muffins, check out these Chocolate Banana Muffins and these Apple Cinnamon Muffins!

Finally, if you make this recipe and decide to share it on Facebook or Instagram, don’t forget to tag me @FromMyBowl + #FromMyBowl! I love seeing your delicious recreations 🙂


Vegan Lemon Poppy Seed Muffins

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5 from 12 reviews

These Lemon Poppyseed Muffins have crispy golden edges and a fluffy, melt-in-your mouth crumb! The perfect breakfast treat. 

  • Author: Caitlin Shoemaker
  • Prep Time: 10 Minutes
  • Cook Time: 27 Minutes
  • Total Time: 37 minutes
  • Yield: 12 Muffins 1x
  • Category: Breakfast
  • Method: Oven
  • Cuisine: American
  • Diet: Vegan



For the Muffins:

  • 2 1/4 cups (280 g) flour, spooned and leveled*
  • 2 teaspoons baking powder
  • 1 teaspoon baking soda
  • 2 tablespoons ground flaxseed
  • 2 tablespoons poppy seeds
  • 1/2 teaspoon salt
  • 3/4 cup (158 g) cane sugar
  • 1 tablespoon lemon zest (about 1 lemon)
  • 1 cup (235 mL) vegan yogurt*
  • 1/4 cup (60 mL) non-dairy milk
  • 1/4 cup (60 mL) neutral oil or vegan butter
  • 2 tablespoons lemon juice (about 1 lemon)
  • 1 tablespoon vanilla extract

For the Lemon Glaze (Optional):

  • 1/2 cup powdered sugar
  • 23 teaspoons lemon juice


  1. Prep: Preheat the oven to 425F and line a muffin tin with paper liners.
  2. Dry Ingredients: Sift the flour, baking powder, and baking soda into a large mixing bowl. Add in the poppy seeds, flaxseed, and salt, then mix until combined. Form a well in the center of the bowl and set aside.
  3. Wet Ingredients: Pour the sugar into a medium bowl, then add in the lemon zest. Use your hand to massage the lemon zest into the sugar – this ensures it gets evenly distributed, and gives a better lemon flavor. Add in the vegan yogurt, milk, oil, lemon juice, and vanilla. Stir until the sugar is dissolved.
  4. Combine: add the wet ingredients to the bowl of dry ingredients and stir just until a slightly lumpy batter forms – the batter will be very thick. Use a spoon or large cookie scoop to fill each muffin liner 7/8 of the way full. 
  5. Bake: Place the muffins in the middle rack of the oven. Bake at 425F for 7 minutes, then, without opening the oven, reduce the temperature to 350F. Continue to bake the muffins for an additional 20 to 22 minutes. The initial raised temperature helps the muffins to rise better and get golden tops.
  6. Lemon Glaze (Optional): If you’d like to make the lemon glaze, combine the powdered sugar and 2 teaspoons of the lemon juice together in a small bowl and whisk until smooth and glossy. Add the remaining teaspoon of lemon juice if the mixture is too thick. Set aside.
  7. Serve & Store: Remove the muffins from the oven and let sit in the baking tray for 1 to 2 minutes, until no “crackling” sounds occur and the muffins have set. Carefully transfer the muffins to a cooling rack, or enjoy warm. Top with lemon glaze just before serving – store any leftover glaze in a sealed jar at room temperature for up to 3 days. Leftover muffins will keep at room temperature for up to 3 days for the best texture, or in the freezer for up to 3 months. Muffins can be reheated in the oven or microwave. I don’t recommend glazing your muffins until right before eating, otherwise the tops will get a little soggy.


  • Flour: Do NOT simply scoop your flour using the measuring cup – go by weight, or use a spoon to fill the cup and then level the top off. Swap up to half of the flour in this recipe with whole wheat flour for a denser, heartier muffin. You can try swapping the flour for gluten-free cup-for-cup flour, but I haven’t tested it. Instead I would recommend this GF Lemon Poppy Seed Cake, which uses a combination of oat flour or almond flour.
  • Other Substitutions: ground flax can be replaced with ground chia seeds. The lemon juice can be swapped with apple cider vinegar, but if you do this don’t skip the lemon zest.

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About the Author

Hey there, I’m Caitlin! I make easy-to-follow, wholesome, and budget-friendly vegan recipes that are mostly gluten-free and refined sugar-free. I’m also an avid yogi, love the great outdoors, am chocolate-obsessed, and enjoy eating almond butter straight off of the spoon.

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  1. What kind of yogurt did you use? Would you increase the milk or flax seeds to substitute the yogurt?

    1. I used an unsweetened cashew yogurt! I think the best substitute would be applesauce or pumpkin puree, plus adding ~1-2 tsp more lemon juice to replace the tang

  2. Made these last night and they came out perfectly moist, fluffy and with a nice golden top. Totally convinced my skeptical roommate (her previous experiences with vegan baked goods were mediocre to say the least). I added the zest of two lemons, but skipped the glaze. Thanks Caitlin!

      1. Hi Kelly! If you want to make the same # of muffins, I’d probably cut the batter in half and start checking for doneness at about half of the stated cook time.