These healthy lemon poppy seed muffins are light and airy, with a delicious lemony flavor. They are an amazing baked treat, best served with a cup of tea for breakfast.

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Muffins don't typically tend to be healthy - and attempts to make them a little healthier don't always work out. But this recipe creates the most lovely, light, fluffy and moist lemon poppy seed muffins.
Using some simple substitutions, we can make amazing muffins with ingredients you probably already keep in your pantry. No special ingredients required.
If you love these lemon muffins, you might also want to check out my healthy banana oat muffins with raisins, Banana Carrot Muffins, Blueberry Protein Muffins, Pumpkin Zucchini Muffins or these easy puff pastry cinnamon rolls.
Ingredients
To make this recipe, you will need Greek yogurt, olive oil, vanilla extract, poppy seeds, white whole wheat flour, lemon (juice + zest), eggs, honey, baking powder, baking soda and salt.
Muffins typically include sour cream, butter and sugar. In this recipe we replace these with Greek yogurt, olive oil and honey. The result is the same good muffins that you're used to, but made with better ingredients.
💡 TIP! If you don't have white whole wheat flour available, you can also use regular all purpose flour.
Instructions
Preheat your oven to 360 °F / 180 °C / 160 °C fan oven. Zest two lemons using a microplane, and squeeze the juice out of one lemon. Measure and prepare the other ingredients.
Combine all the wet ingredients in a bowl; eggs, Greek yogurt, olive oil, vanilla extract, honey, lemon juice.
Then, add the dry ingredients; baking powder, baking soda, salt, flour and lemon zest. Mix the ingredients together until just combined.
Place muffin liners in a muffin pan. Fill the liners about ⅔ full of the batter. Place them in the oven, and bake for about 17 min, or until a skewer or toothpick inserted in the middle comes out clean.
Discover more healthy snack recipes.
Top tips
Here are my best advice to make the best healthy lemon poppy seed muffins:
- Don't over mix the batter! Only stir until the ingredients are just combined.
- Fill the muffin liners ⅔ full. This prevents them from expanding too much, and gives them a nice shape.
- Use a toothpick or a skewer inserted in the middle of the lemon poppy seed muffins to ensure that they have cooked through.
- The muffins can burn quickly, so keep an eye on them. Overcooked muffins are dry and unpleasant.
Serving suggestions
- Top the muffins with your favorite icing if you want an extra sweet treat.
- Iced Chai Latte with Almond Milk - Serve the muffins with your morning coffee.
- Strawberry Basil Sauce - Add some strawberry sauce on top, because fruits are delicious.
- Cilantro tea - The muffins go really well with this easy tea made with fresh herbs.
Variations
Fruity: Add some finely diced fresh fruit or berries, such as raspberries or oranges.
Vegan: Use a vegan egg substitute and vegan yogurt for a vegan friendly version of the recipe.
Double lemon: Double up on the lemon zest, or coat the muffins with a lemon flavored icing or frosting if you want to increase the lemon flavor.
Leftovers
Muffins store really well. You can keep them in an airtight container in your pantry for up to 5 days, or freeze them for up to 12 months.
Defrost the frozen muffins before serving them. They are usually served at room temperature, but you can choose to warm them up for a few seconds in a microwave if you prefer warm muffins.
As they can keep for a very long time, this recipe is perfect for batch baking! Simply double or triple the recipe to make a larger amount, and freeze the lemon poppy seed muffins for a rainy day.
Frequently asked questions
Substitute healthier ingredients. Replace sour cream with Greek yogurt, sugar with honey and butter with olive oil.
Yes. You can avoid using liners by spraying the muffin pan well with a cooking spray. This will prevent the muffins from sticking to the pan.
Recipe
Healthy Lemon Poppy Seed Muffins
Ingredients
- 2 cups white whole wheat flour (or all purpose flour) (500 ml / 250 g)
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- ½ teaspoon salt
- ½ cup honey (120 ml)
- ½ cup olive oil (120 ml)
- ½ cup Greek yogurt (120 ml)
- 1 teaspoon vanilla extract
- 2 eggs
- 2 lemons (juice from 1 + zest from 2)
- 3 tablespoons poppy seeds
Instructions
- Preheat your oven to 360 °F / 180 °C / 160 °C fan oven.
- Zest two lemons using a microplane, and squeeze the juice out of one lemon. Measure and prepare the other ingredients.
- Combine all the wet ingredients in a bowl; eggs, Greek yogurt, olive oil, vanilla extract, honey, lemon juice.
- Then, add the dry ingredients; baking powder, baking soda, salt, flour and lemon zest. Mix the ingredients together until just combined.
- Place muffin liners in a muffin pan. Fill the liners about ⅔ full with the batter.
- Place them in the oven, and bake for about 17 min, or until a skewer or toothpick inserted in the middle comes out clean.
Video
Notes
- Don’t over mix the batter! Only stir until the ingredients are just combined.
- Fill the muffin liners ⅔ full. This prevents them from expanding too much, and gives them a nice form.
- Use a toothpick or a skewer inserted in the middle of the lemon poppy seed muffins to ensure that they have cooked through.
- The muffins can burn quickly, so keep an eye on them. Overcooked muffins are dry and unpleasant.
- Muffins store really well. You can keep them in an airtight container in your pantry for up to 5 days, or freeze them for up to 12 months.
Patti
Hi, what are your thoughts on replacing the flour with almond flour?
Tonje
I have not tried making these with almond flour yet, so I'm not sure. Let me know how it goes if you give it a try!