Healthy Lemon Poppy Seed Muffins

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Looking for a healthy lemon poppy seed muffin recipe? You’ve come to the right place! These delicious lemon poppy seed muffins are the perfect breakfast treat to enjoy without the guilt! No refined sugar and made with good quality ingredients.

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Frosted lemon poppy seed muffin on top of stack of lemon slices.

Do you love a moist, delicious muffin, but not all the sugar and calories that come with a coffee shop or bakery-style muffin? Good news! These healthy lemon poppy seed muffins have all the flavor of bakery-style lemon muffins, without all the junk.

Made without refined sugar, this lemon poppy seed muffins recipe has been adapted to keep all the flavor and moistness that a traditional coffee shop muffin has, but without all the sugar.

Wet ingredients for lemon poppy seed muffins.

Dry ingredients for lemon poppy seed muffins.

What do I need to make lemon poppy seed muffins?

Here’s a quick-reference checklist of the ingredients you’ll need to make these lemon muffins:

All purpose flour
Granular sweetener – I like Whole Earth Granular Monk Fruit Sweetener, or Lakanto
Baking Powder
Baking Soda
Salt
Eggs
Plain Greek Yogurt
Milk – plant or dairy
Unflavored coconut oil
Juice and zest of a lemon
Poppy seeds
For Glaze: lemon juice and Swerve Powdered Sugar Substitute

For exact ingredient amounts and full recipe instructions be sure to reference the recipe at the bottom of this post. Thank you!

Muffin batter with lemon zest, juice and poppy seeds at the top, with whisk on the side.

Lemon poppy seed muffin batter in mixing bowl.

How do I make healthy lemon poppy seed muffins?

Start by mixing the dry ingredients together in one bowl; the flour, sweetener, baking powder, baking soda and salt. Set this mixture off to the side.
Next, combine the wet ingredients; Eggs, yogurt, milk and oil. Gradually add the dry ingredient mixture to the wet ingredients to create the muffin batter.
Then, add in the lemon juice, lemon zest and poppy seeds. Stir to combine.

Lemon poppy seed muffin batter in cupcake pan.

Add the muffin batter to a cupcake pan that has been lined with either paper liners or silicone liners. Pro-Tip: silicone baking liners are fantastic! Unlike paper liners, which often need to be sprayed with non-stick baking spray, silicone baking cups are completely non-stick and your muffins pop right out.
Bake the muffins at 400 degrees for 16-18 minutes or until the muffins are golden brown on top. To test muffins for doneness, insert a toothpick – if the toothpick comes out clean and crumb-free the muffins are done.

Lemon glaze in bowl, with baked muffins on cooling rack.

Swerve powdered sugar alternative used to make lemon glaze for muffins.

Once the lemon poppy seed muffins have come out of the oven and cooled slightly, you can add a lemon glaze. (Note: it’s okay of the muffins are still warm.)
To make the lemon glaze I used Swerve Confectioners Sugar Substitute. I use Swerve often when I want to keep recipes with low or no refined sugar. Drizzle the glaze over the top of each muffin. Let the glaze set for a few minutes and enjoy!

Love baking muffins? Check out some of my other muffin recipes:

Glazed lemon poppy seed muffins on cooling rack with lemon slices.

FAQ’s about baking poppy seed muffins:

What does lemon poppy seed muffin taste like?

Lemon poppy seed muffins taste like a tender vanilla cake with a subtle lemon flavor. The poppy seeds are flavorless, but add a slight crunch.

What are lemon poppy seed muffins made of?

Lemon poppy seed muffins include flour, sweetener, baking powder, baking soda, salt, eggs, yogurt, milk, coconut oil, lemon juice, lemon zest and poppy seeds.

How do I make muffins healthier?

There are a few ingredient swaps to make muffins healthier. First, a portion or all of the oil for plain Greek yogurt, and instead of using refined/granular sugar, use a granular monk fruit sweetener. You can also use whole wheat or oat flour as a substitute for all-purpose flour.

Do you love lemon treats? Check out some of my other lemon recipes:

If you loved these healthy muffins, check out some of my other healthier muffin recipes:

Healthy cranberry orange muffins, half of muffin held over top of muffin tin. — **Healthy Cranberry Orange Muffins**

Stack of 3 double chocolate muffins, garnished with chocolate chips. — **Healthy Cranberry Orange Muffins**

Lemon Poppy Seed Muffins

Yield: 12 muffins

Prep Time: 15 minutes

Cook Time: 18 minutes

Total Time: 33 minutes

Looking for a healthy lemon poppy seed muffins recipe? These moist, delicious lemon poppy seed muffins are made without refined sugar, but still have amazing flavor!

Ingredients

2 c. all-purpose flour
1/3 c. granular monk fruit sweetener, like Whole Earth or Lakanto
1 1/2 tsp. baking powder
1/2 tsp. baking soda
1/4 tsp. salt
3/4 c. plain Greek yogurt, I like Fage full-fat Greek yogurt
3/4 c. milk, dairy or plant-based
2 eggs
2 tbsp. unflavored coconut oil
1/4 c. fresh squeezed lemon juice (juice of 1 lemon)
1 Tbsp. lemon zest (zest of 1 lemon)
1 Tbsp. poppy seeds

Lemon Glaze:

2 tbsp. fresh squeezed lemon juice (juice of 1/2 lemon)
1/2 c. Swerve confectioners sugar substitute

Instructions

Preheat oven to 400 degrees. Line a muffin tin with non-stick silicone baking cups or paper liners that have been sprayed with non-stick baking spray. Set prepared pan aside.
In a mixing bowl, whisk together the dry ingredients; flour, sweetener, baking powder, baking soda and salt. Set aside.
In a second bowl, whisk together the wet ingredients; yogurt, milk, eggs and oil. Gradually add the dry ingredient mixture to the wet ingredients, using a whisk to combine. Batter will be slightly thick.
Add in the lemon juice, lemon zest and poppy seeds. Stir to combine.
Spoon the batter into the prepared muffin tin, filling each cup to nearly full.
Bake the muffins at 400 degrees for 16-18 minutes or until toothpick inserted into a muffin comes out clean and crumb-free. Tops of muffins will be golden brown.
Remove from oven and let cool while you mix the lemon glaze. Combine the Swerve confectioners sugar substitute with 2 tbsp of lemon juice, stirring until smooth. Drizzle over the tops of each muffin. Enjoy!

Notes

Storage: muffins can be kept at room temperature, however, they will only keep for 2-3 days at most. For best results, store muffins in an airtight container in the refrigerator. Kept refrigerated, muffins will last 5-7 days.

Freezing: these muffins freeze well, and make for great make-ahead snacks and breakfasts. To freeze, individually wrap or store in an airtight container. Frozen, the muffins will last up to 3 months. To thaw, you can either let thaw at room temperature (good for overnight) or unwrapped in microwave on defrost setting at 30 second increments.

Nutrition Information:

Yield: 12 Serving Size: 1 muffin
Amount Per Serving: Calories: 176Total Fat: 5gSaturated Fat: 3gTrans Fat: 0gUnsaturated Fat: 2gCholesterol: 36mgSodium: 196mgCarbohydrates: 25gFiber: 1gSugar: 8gProtein: 8g

Lemon poppy seed muffins topped with glaze and on cooling rack with lemon slices.

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