Lemon Poppy Seed Muffins

These healthyish lemon poppy seed muffins made with oat flour are a delicious and easy breakfast or snack recipe. Perfect for making ahead!

Lemon poppy seed muffins

Ingredients needed

  • Flour. To make these muffins a little healthier, I swap out some of the all-purpose flour for oat flour. The oat flour adds texture and extra fiber. Use all all-purpose flour if you prefer.
  • Baking powder.
  • Salt.
  • Greek yogurt. Sour cream can be substituted.
  • Canola oil. Any vegetable oil can be used. Avocado oil is a great substitution. Melted butter can also be used.
  • Sugar. I like using brown sugar but coconut sugar or regular granulated sugar will work well too.
  • Eggs. 
  • Poppy seeds. 
  • Lemon zest and fresh lemon juice. Using a few tablespoons of lemon zest gives the best lemon flavor to these muffins. The lemon juice is used for the lemon glaze.
  • Powdered sugar/icing sugar.

How to make lemon poppy seed muffins

The batter can be made in one bowl making the recipe even easier. Whisk the dry ingredients together in a large bowl then add the oil, eggs, egg yolks, yogurt, poppy seeds and lemon zest. Stir until the batter is smooth and creamy. Line a muffin pan with paper liners/cupcake liners then fill the cups three quarters of the way full. Place in the oven and bake at 180ºC/350ºF for 20-25 minutes until the muffins are risen, golden brown and a toothpick or cake tester inserted comes out clean. Once baked, the muffins can be cooled in the muffin tin for 20 mins then removed and allowed to cool on a wire rack until room they are room temperature. I like finishing them with a a drizzle of lemon glaze but this is optional.

Ingredients for lemon poppy seed muffins

Making ahead and freezing

  • How to store muffins:  These muffins can be kept in an airtight container for up to 3 days at room temperature or 5 days in the fridge. Allow to come to room temperature before serving.
  • Can you freeze muffins? Baked and cooled muffins can be transferred to a ziploc bag and frozen for up to 3 months. Thaw at room temperature before serving.
Lemon poppy seed muffins


What are poppy seed muffins made of?

These lemon poppy seed muffins consist of flour (oat and all-purpose flour), baking powder, salt, sugar, lemon zest, poppy seeds, Greek yogurt, oil and eggs.

Is poppy seed and chia seeds the same?

No, poppy seeds and chia seeds are two different kinds of seeds. Chia seeds have a higher fiber content than poppy seeds but they are also a little bigger and crunchier.

How to make muffins moist

The addition of canola oil, plain yogurt and the extra egg yolk means these muffins are tender and moist and will stay that way for up to 5 days.

Muffin recipes

  1. Cinnamon brown sugar pumpkin muffins
  2. Easy healthy blueberry muffins
  3. Zucchini bread muffins with pecan streusel

Lemon Poppy Seed Muffins

These healthyish lemon poppy seed muffins made with oat flour are a delicious and easy breakfast or snack recipe. Perfect for making ahead!
5 from 1 vote
Print Pin Rate
Course: Baked goods, Breakfast
Cuisine: American
Keyword: Lemon poppy seed muffins, muffin recipes, muffins
Prep Time: 10 minutes
Cook Time: 25 minutes
Total Time: 35 minutes
Calories: 204kcal
Author: Alida Ryder
Servings: 12


  • 1 cup oat flour
  • 1 cup flour regular/all purpose
  • 2 tsp baking powder
  • 1 tsp salt
  • 3/4 cup brown sugar
  • 1 tbsp poppy seeds
  • 1 cup plain yogurt
  • 3/4 cup canola oil
  • zest of 2 lemons
  • 3 extra-large eggs + 1 egg yolk
  • 1 tbsp lemon juice
  • 2 tbsp milk

Lemon glaze (optional)

  • 5 tbsp icing sugar sifted
  • 1-2 tbsp lemon juice (depending on how thick/thin you want the glaze)


  • Preheat the oven to 180°C/350°F and line a 12-hole muffin pan with paper liners.
  • Whisk all the dry ingredients together in a large mixing bowl. Add the wet ingredients and whisk until the batter is smooth and creamy.
  • Fill muffin liners 3/4 of the way full. Place in the oven and bake for 20-25 minutes until golden brown and a toothpick inserted comes out clean.
  • Remove the baked muffins from the oven and allow to cool completely.
  • Whisk together the glaze ingredients then drizzle over the cooled muffins.


Calories: 204kcal | Carbohydrates: 23g | Protein: 5g | Fat: 11g | Saturated Fat: 1g | Cholesterol: 1mg | Sodium: 205mg | Potassium: 138mg | Fiber: 2g | Sugar: 7g | Vitamin C: 1mg | Calcium: 83mg | Iron: 1mg

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  1. Hello Alida! I made these muffins this afternoon and weighed all ingredients; overall I liked them (great texture!) altho thought the canola oil proportion was a little too much b/c the muffin texture/flavor and muffin paper cups were a bit oily, so next time I’ll cut back maybe 2Tbls…..your thoughts? Also, while still warm (b/c I couldn’t wait for them to cool), the first muffin released from the paper cup perfectly, but the cooled ones stuck to the paper cups quite a bit, losing about 1/4 of the muffin bottom (not to worry, I scraped it off and ate it:) Do you why that happened and especially with a fair amount of oil? Thank you for your input!

    1. You could definitely add only 1/2 cup of oil. I found 1/2 cup left the muffins a little on the drier side but it could be that my oat flour absorbs more liquid. Very strange that they stuck once cool, it’s usually the opposite for me. What sweetener did you use?

      1. Hi Alida,
        I used raw granulated sugar. I noticed after baking that your photo shows what looks like either light or dark brown sugar….is that correct?

        Also, next time I make these, I’ll try some variations with the canola oil, using a little less and maybe try half butter/half oil. Thanks again for the delicious recipe!!

    2. Disregard the above muffin-sticking comment…..the following morning, the muffins released from paper muffin cups cleanly!