Lemon Poppy Seed Muffins (Gluten Free + No refined sugar)

lemon-poppy-seed-muffins-(gluten-free-+-no-refined-sugar)

Ana Ankeny

By: Ana Ankeny Updated: 5/6/22

Enjoy these light and moist Lemon Poppy Seed Muffins for the perfect breakfast treat. Made gluten-free and with no refined sugar, these muffins are bursting with lemony flavors from fresh lemon zest and juice!

Overhead view of a six count muffin tin holding five lemon poppy seed muffins, one muffin outside the fin drizzled with lemon glaze.

Almost too good to be true

These unbelievably tender lemon poppyseed muffins make breakfast something to look forward to. The addition to yogurt adds moisture and a delicious tang, reminiscent of pound cake. But because we use only honey to sweeten them they’re perfect for breakfast, brunch, or with afternoon tea. Drizzling them with the optional glaze makes them dessert-like but they’re plenty delicious without it if you want to keep them refined sugar-free.

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A lemon poppy seed muffin broken in half sitting on two white paper liners showing the fluffy inside texture, lemon glaze on top.

Ingredients for Lemon Poppy Seed Muffins

  • Eggs
  • Honey – use local honey if available to you, for an easy to find honey, we recommend this one
  • Yogurt – we use plain, unsweetened yogurt, but use a coconut milk-based yogurt for a non-dairy muffin option. May also sour cream, if desired.
  • Avocado oil
  • Pure vanilla extract
  • Lemon – using both the lemon zest and fresh lemon juice bumps up the natural lemon flavor in these mouth-watering and tender muffins
  • Gluten free 1:1 flour – We recommend Bob’s Red Mill 1:1 Gluten-Free Flour or King Arthur Measure for Measure Gluten-Free Flour. Substitute all-purpose flour if you don’t need these to be gluten-free.
  • Baking powder
  • Baking soda
  • Salt
  • Poppy seeds – we use black poppy seeds for a more pronounced flavor and a pretty contrast of color that’s the hallmark of a lemon poppyseed muffin

Optional Glaze:

  • Lemon – Use both the zest and juice for extra lemon flavor
  • Powdered sugar – use your favorite powdered sugar, we recommend this one
  • Milk of choice – use regular milk or non-dairy for a dairy-free muffin option
A close up side view of a lemon poppy seed muffin on a white countertop with lemon glaze sliding the sides.

How to make these lemon poppy seed muffins

  1. Preheat oven to 350 F. Line a muffin pan with paper muffin liners (we recommend using reusable liners such as these) or generously spray the muffin tin with cooking spray then set aside.
  2. In a large bowl, whisk together the eggs, honey, yogurt, oil, vanilla, lemon zest, and lemon juice. 
  3. To the wet mixture, add the gluten-free flour, baking powder, baking soda and salt. Stir well until all of the dry ingredients are incorporated. Fold in the poppy seeds.
  4. Evenly fill 12 muffin wells with the muffin batter. Bake for 16-18 minutes or until a toothpick inserted into center comes out clean. 
  5. Place the muffin pan on a wire rack to cool for 10 minutes. After 10 minutes, remove the muffins from the pan to the wire rack to cool completely.
  6. Store any leftovers in an airtight container at room temperature for up to 2 days or in the freezer for up to 3 months.

Optional Glaze (omit for refined sugar-free option)

  1. In a small bowl, combine to lemon juice, powdered sugar, milk, and lemon zest. Whisk until smooth Add more powdered sugar (1 tablespoon at a time) or more milk (1 teaspoon at a time) and continue to whisk until a drizzly consistency is reached. Pour or drizzle over cooled muffins.
Overhead view of all ingredients for lemon poppy seed muffins arranged together in small bowls and measuring cups.
Overhead view of lemon poppy seed muffin batter in a clear bowl with a white spatula in batter.
A six muffin tin holder holding six lemon poppy seed muffins in white paper liners.

Lemon Poppy Seed Muffin FAQ

Can I use all-purpose flour?

If you don’t need your muffins to be gluten-free, you can swap the gluten-free flour for all purpose flour in equal amounts.

Can these Muffins be made Egg-Free or vegan?

We have not tested this recipe using gluten-free flour with an egg substitute in addition to dairy-free yogurt so we can’t say for sure how they would turn out. However, if you try it we’d love to know how they turned out for you – just leave us a comment below.

Are there any Health benefits of poppy seeds?

Poppy seeds have recently received some positive press for their potential health benefits which you can read more about in this article. While our lemon poppy seed muffin recipe calls for only one tablespoon of poppyseeds, they are a good source of manganese and copper. If you’re looking for another delicious way to enjoy them, be sure to try our Strawberry Poppy Seed Chicken Salad recipe.

How do I store muffins?

Once completely cooled, you can store lemon poppy seed muffins in an airtight container at room temperature for up to 2 days. For longer storage, we suggest freezing them.

Can I freeze lemon poppy seed muffins?

Absolutely! To free, place cooled muffins in the refrigerator until well-chilled (about 4 hours) then transfer to a freezer-safe container or large zip-top bag in a single layer and place in the freezer for up to 3 months. For best results, we recommend removing the desired number of muffins from the freezer and thawing in covered container in the refrigerator or on the counter overnight. If you’d like, you can warm them in the microwave or toaster oven for a few seconds before enjoying.

How do I meal prep this muffin recipe?

These lemon poppyseed muffins can be prepared, cooled and either stored in the refrigerator or freezer until ready to use.

A single lemon poppy seed muffin topped with lemon glaze and sprinkled with lemon zest on a fanned out white muffin liner sitting on two stacked up white plate.

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A single lemon poppy seed muffin broken in half sitting on two white muffin liners to show inside texture.

Recipe

Lemon Poppy Seed Muffins (Gluten Free + No refined sugar)

Light and fresh, these Lemon Poppy Seed Muffins make for great breakfast addition! Easily make them ahead for a breakfast meal prep and easy on-the-go breakfasts or snacks.

Prep: 10 minutesCook: 16 minutesTotal: 26 minutes

Ingredients

  • 2 large eggs
  • ½ cup honey
  • ¾ cup plain yogurt (substitute non-dairy yogurt, for dairy-free; May also use sour cream)
  • ¼ cup avocado oil (or other light-tasting oil)
  • 1 tablespoon pure vanilla extract
  • 1 tablespoon lemon zest
  • 2 tablespoons lemon juice
  • 2 ¼ cups 1:1 gluten-free flour (311g; we recommend Bob’s Red Mill 1:1 Gluten-Free Baking Flour or King Arthur Measure-for-Measure)
  • 2 ½ teaspoons baking powder
  • 1 teaspoon baking soda
  • ¼ teaspoon fine salt
  • 1 ½ tablespoons poppy seeds

Optional Lemon Glaze (omit for no-refined sugar)

  • 1 medium lemon, juiced and zested
  • ¼ cup powdered sugar 
  • 12 tablespoons milk of choice (use non-dairy milk for dairy-free)

Instructions

  1. Preheat the oven to 350 F. Line a muffin pan with paper muffin liners (we recommend using reusable liners such as these) or generously spray the pan with cooking spray then set aside.
  2. In a large bowl, whisk together the eggs, honey, yogurt, oil, vanilla, lemon zest, and lemon juice. 
  3. To the wet mixture, add the gluten-free flour, baking powder, baking soda and salt. Stir well until all of the dry ingredients are incorporated. Fold in the poppy seeds.
  4. Evenly fill 12 muffin wells with the muffin batter. Bake for 16-18 minutes or until a toothpick inserted into center comes out clean. 
  5. Place the muffin pan on a wire rack to cool for 10 minutes. After 10 minutes, remove the muffins from the pan to the wire rack to cool completely.
  6. Store any leftover muffins in an airtight container at room temperature for up to 2 days or in the freezer for up to 3 months.

Optional Glaze:

  1. In a small bowl, combine to lemon juice, powdered sugar, milk, and lemon zest. Whisk until smooth Add more powdered sugar (1 tablespoon at a time) or more milk (1 teaspoon at a time) and continue to whisk until a drizzly consistency is reached. Pour or drizzle over cooled muffins.

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Notes

Regular all-purpose flour may be used in place of gluten-free flour if you don’t need these to be gluten-free.

Nutrition Information

  • Serving Size: 1 muffin
  • Calories: 210
  • Fat: 6 g
  • (Sat Fat: 1 g)
  • Sodium: 135 mg
  • Carbohydrate: 36 g
  • (Fiber: 1 g
  • Sugar: 12 g)
  • Protein: 3 g
  • Cholesterol: 31 mg

Dietary

© The Real Food Dietitians


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A single lemon poppy seed muffin topped with lemon glaze and lemon zest sitting on a fanned out white muffin liner placed on two stacked up small plates.

All photos and content are copyright protected. Please do not use our photos without prior written permission. If you wish to republish this recipe, please rewrite the recipe in your own unique words and link back to the source recipe here on The Real Food Dietitians. Thank you!

Photo Credit: The photos in this blog post were taken by Rachel of Half Acre House

Ana Ankeny

Ana Ankeny

Ana is a recipe developer, fellow food blogger, and Pinterest manager. She lived in Blue Earth, MN with her husband and four boys. She’s on a mission to turn highly-processed meals into real-food meals…one dish at a time! She loves spending time with her family, powerlifting, traveling, and being in the kitchen.

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