Vegan Lemon Poppy Seed Muffins

stack of 3 muffins with the top one cut in half on small white plate

5 from 11 reviews

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



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.

Keywords: vegan lemon muffins, lemon poppyseed muffins, dairy free lemon poppyseed muffins