Made with fresh lemon juice, lemon zest, and yogurt, these healthy lemon poppy seed muffins are light, fluffy, and bursting with zesty citrus flavor. With an optional lemon glaze, these lemon muffins can easily be enjoyed as a simple breakfast or sweet treat and are a healthy option the whole family will enjoy.

What You’ll Need for Lemon Poppy Seed Muffins

While traditional lemon muffins are made without yogurt, I opted to add yogurt to this recipe in an effort to add a small boost of protein and a bit of moisture at the same time. Here’s what you’ll need to make them:

Flour: All-purpose flour will give you the best results. If you want to make them gluten-free, it’s best to use 1-to-1 gluten-free flour, I wouldn’t recommend using almond or coconut flour in this recipe.
Lemon: Be sure to use fresh lemon juice and fresh lemon zest, lemon concentrate won’t provide the same lemon flavor.
Yogurt: It’s best to use plain yogurt for these lemon poppy seed muffins because Greek is a little too thick. If you must use Greek yogurt, you’ll need to add a bit of extra milk to loosen the batter and, while I used unsweetened in my recipe, you could certainly use vanilla yogurt for an extra punch of flavor. You can also use sour cream if you don’t have any yogurt on hand.
Eggs: This recipe calls for 2 whole eggs, if you want to make the muffins egg-free, you can replace the eggs with a flax egg or chia egg instead.
Butter: A little bit of butter paired with the yogurt gives these muffins the perfect level of moisture.
Sugar: While you could use honey or a sugar alternative, I find white sugar works the best in these muffins and the nutrition differences between sweeteners are in fact minimal, so don’t worry about that. Plus, for an extra touch of sweetness, you can add a simple glaze to these lemon muffins.
Poppy Seeds: While these are technically optional, you can’t make lemon poppy seed muffins without poppy seeds!

To Make them Gluten-Free: Replace the all-purpose flour with 1-to-1 gluten-free flour.

To Make them Dairy-Free: Replace the yogurt with coconut yogurt and use olive oil instead of butter.

To Reduce the Sugar Content: Omit the glaze completely as the muffins are incredibly tasty without it.

How to Make Lemon Poppy Seed Muffins with Yogurt

These muffins are incredibly easy to make and come down to 5 primary steps:

Combine the dry ingredients. Add the dry ingredients; flour, baking powder, baking soda, salt, and poppy seeds, to a mixing bowl and stir to combine.
Combine the wet ingredients. Add the wet ingredients (and sugar) to a large bowl and stir until well combined. Adding sugar to the wet ingredients helps to inhibit the gluten-forming proteins and provides a better texture to create fluffy and tender muffins.
Mix the batter. Add the dry ingredients to the wet ingredients and mix until well combined and then divide the batter evenly across a muffin tin.
Bake the muffins. Transfer the muffins to the oven and bake until light and fluffy.
Add the lemon drizzle. Once baked, allow the muffins to cool completely before adding the lemon sugar drizzle!

If desired, you could also add some fresh or frozen blueberries to make them extra seasonal and add a bit of fiber at the same time.

How to Make them Bakery-Style Muffins

This recipe makes 12 large muffins or 24 mini muffins depending on what size you want them to be. If you want to make these bakery-style muffins, use large muffin liners, and fill each muffin cup with an additional 25% of batter to create a total of 9 muffins instead of 12, and increase the baking time by 3-5 minutes or until a toothpick comes out clean.

Are poppy seed muffins good for you?

Absolutely! Poppy seeds are primarily a source of fat, as well as some fiber and protein; one tablespoon of poppy seeds contains 3.7 grams of fat, 1.6 grams of protein, 2.5 grams of carbohydrate, and 1.7 grams of fiber(1). Poppy seeds are also a good source of B vitamins, manganese, calcium, magnesium, and iron. Including poppy seeds in muffins can help to increase the content of healthy fats, dietary fiber, and essential micronutrients.

How long do lemon poppy seed muffins last?

Once baked, these lemon poppy seed muffins store well in an airtight container or bag in the pantry or fridge for up to 5 days or in the freezer for up to 3 months.

How to reheat frozen poppy seed muffins?

If frozen, allow the muffins to thaw at room temperature before eating, or heat them in the microwave for about 30-45 seconds until warm and fluffy, or reheat them directly from frozen for 1-2 minutes.

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