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    Home » Breakfast

    Gluten Free Lemon Poppy Seed Muffins

    Updated: Oct 18, 2025 by Tiffany · This post may contain affiliate links · 3 Comments.

     

     

    Jump to Recipe Print Recipe

    These gluten free lemon poppy seed muffins are just perfect! Trust me, I've done the research.  

    Lemon poppy seed muffins have always been one of my favorite breakfast treats.  I used to visit a bakery near my house almost every morning to get one of their oversized lemon poppy seed muffins topped with crunchy sugar. Yum! 

    This easy recipe is a pretty close copy of those delicious bakery style muffins, filled with bright lemon flavor.  Hope you love them as much as I do!

    Half of a gluten free lemon popy seed muffin served on a blue plate.

    If you love baking homemade muffins, make sure to check out all of my favorite gluten-free muffins.

    Jump to:
    • Ingredient Notes
    • Substitutions
    • How to Make Gluten Free Lemon Poppyseed Muffins
    • Baking Tip
    • How to Store & Reheat Muffins
    • More gluten-free muffin recipes to try:
    • Recipe

    Ingredient Notes

    These easy lemon muffins require just a handful of simple ingredients that can be found in any grocery store.  The recipe is both gluten free and dairy free as written.

    Ingredients for gluten free lemon poppy seed muffins on a metal baking sheet.
    • Gluten-Free Flour Blend - I use Bob's Red Mill gluten free 1-to-1 flour in most of my muffin recipes.  You can use your favorite brand, but the results may vary since all gluten free flour blends are a little different in their makeup. If you use another type of gluten free flour, ensure it contains xanthan gum.
    • Poppy Seeds - While the poppy seeds don't add anything to the flavor of the muffin, they are one of the main ingredients of this traditional combo.
    • Egg - Just one egg in this muffin recipe. I haven't tried an egg replacement, but I think replacing the egg with either applesauce or flax eggs would work. 
    • Non-dairy milk - I use either coconut milk or oat milk, but any plant based milk will work.  If you're not dairy free, use regular milk in the same measure.
    • Fresh Lemon Juice and Fresh Lemon Zest  - Lemon juice and zest provides all of the fresh lemon flavor in these muffins.  One fresh lemon will provide enough zest and juice for this recipe.  

    See the recipe card for complete list with measurements.

    Substitutions

    • Not dairy free - If you're not dairy free, use regular milk in place of non-dairy milk in the same measure.
    • Make it Vegan / Egg Free - I haven't tried it, but I'd suggest replacing the egg with ¼ cup of unsweetened applesauce or a single flax egg.  You won't get the rise that you get from the egg, because there are no bubbles being beaten into the batter so the muffins will be a little more dense after baking.  But the flavor should still be wonderful.
    • No refined sugar - If you're avoiding refined sugar you can replace the ½ cup of sugar in this recipe with ⅓ cup of honey. You will also need to lower the temperature by 25 degrees, since honey will brown faster than regular sugar.

    How to Make Gluten Free Lemon Poppyseed Muffins

    With all of my muffin recipes, I always use the muffin method for mixing.  The muffin method is a fool proof way to get fluffy muffins with gorgeous tall muffin tops.  The best part is, you only need two bowls and a whisk - no electric mixer needed.

    Before you begin mixing, line a 6-cup muffin tin with muffin liners.

    Flour, sugar, baking powder, salt, poppy seeds and lemon zest combined together in a large white bowl.

    STEP 1: Combine the gluten free  flour, sugar, baking powder, salt, poppy seeds
    and lemon zest in a large bowl.  Whisk together.

    A single egg whisked until frothy in a small white bowl.

    STEP 2: In a separate bowl, whisk the egg until it is frothy like soap bubbles.

    Oil, milk and lemon juice being whisked into the beaten egg in a small white bowl.

    STEP 3: Add the oil, milk and lemon juice to the egg and whisk until well combined.

    Wet ingredients being poured into the bowl of dry ingredients.

    STEP 4: Add the wet ingredients into the bowl of dry ingredients.

    Unbaked lemon poppy seed muffin batter in a large white bowl.

    STEP 5: Fold the batter together about 15 strokes until just combined, being careful not to over mix.

    Divide the batter into lined muffins cups and bake. This recipe makes 6 regular sized muffins or 12 mini muffins.

    Baking Tip

    To check for done: gently poke the top center of one muffin with your finger. If it springs right back it is baked through. If it leaves an indentation, bake another 2 minutes and recheck.

    A sliced gluten free lemon poppy seed muffin on a blue plate.

    How to Store & Reheat Muffins

    Store your leftover muffins in an airtight container at room temperature for up to 3 days.  To reheat, place one muffin the microwave for about 15 seconds.

    You can also freeze these muffins to eat later.  Wait until the muffins are completely cooled, then wrap them individually in plastic wrap and place them in a freezer bag or container.  Freeze for up to 3 months.  To enjoy, simply defrost overnight in the refrigerator and then reheat in the microwave until warm.

    More gluten-free muffin recipes to try:

    • Closeup of a lemon blueberry muffin with a bite taken out.
      Gluten Free Lemon Blueberry Muffins
    • A closeup of a banana nut muffin with a bite taken out.
      Gluten Free Banana Muffins
    • gluten free cranberry orange muffins
      Gluten Free Cranberry Orange Muffins
    • Freshly baked gluten free blackberry muffins sitting on a plate with a few fresh blackberries.
      Gluten Free Blackberry Muffins

    If you try this recipe, please leave a 🌟🌟🌟🌟🌟 star rating and let me know how you liked it in the comments below.

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    Recipe

    Gluten free lemon poppy seed muffin on a blue plate.

    Gluten Free Lemon Poppy Seed Muffins

    These gluten free lemon poppy seed muffins are filled with the bright flavor of fresh lemons. They are a perfect treat to start of your day!
    Author: Tiffany
    5 from 4 votes
    Print Pin Rate
    Course: Breakfast
    Cuisine: American
    Prep Time: 10 minutes minutes
    Cook Time: 28 minutes minutes
    Total Time: 38 minutes minutes
    Servings: 6
    Calories: 220kcal
    Prevent your screen from going dark

    Ingredients

    • 1 Cup +3Tbsp Gluten Free 1-to-1 Flour Blend I use Bob's Red Mill
    • 1 ¼ teaspoon Baking Powder
    • ¼ teaspoon Salt
    • 1 Tablespoon Poppy Seeds
    • ½ Cup Sugar
    • 1 Tablespoon Lemon Zest from 1 lemon
    • 1 Egg
    • 3 Tablespoon Oil
    • 6 Tablespoon Non Dairy Milk
    • 1 Tablespoon Lemon Juice from 1 lemon
    • 1 Tablespoon Turbinado Sugar optional for the tops
    US Customary - Metric

    Instructions

    • Preheat oven to 375 °F (191 °C) degrees. Line a muffin tin with 6 paper cups.
    • In a large bowl, combine flour, baking powder, salt, poppy seeds, sugar and lemon zest. Whisk together to mix. Set aside.
      1 Cup +3Tbsp Gluten Free 1-to-1 Flour Blend, 1 ¼ teaspoon Baking Powder, ¼ teaspoon Salt, 1 Tablespoon Poppy Seeds, ½ Cup Sugar, 1 Tablespoon Lemon Zest
    • In a second smaller bowl, crack your egg. Whisk the egg until it's frothy, like soap bubbles.
      1 Egg
    • Add the oil, milk and lemon juice to the egg. Whisk to combine.
      3 Tablespoon Oil, 6 Tablespoon Non Dairy Milk, 1 Tablespoon Lemon Juice
    • Pour the wet ingredients into the dry. Fold together with a spatula about 10-15 strokes.
    • Divide the batter into the 6 muffin cups. Sprinkle the tops with coarse sugar.
      1 Tablespoon Turbinado Sugar
    • Bake in preheated oven for 26-28 minutes until tops spring back when gently poked.
    • Cool in the pan for 5-10 minutes, then serve.

    Notes

    For mini muffins, use a 12-muffin pan lined with mini muffin cups.  Bake for 20-22 minutes at 375 degrees.
    STORAGE: Store leftover muffins in an airtight container at room temperature for up to 3 days.
    FREEZING: Once muffins have cooled to room temperature, individually wrap each muffin in plastic wrap and place in an airtight container.  Freeze for up to 3 months.  Thaw overnight in the refrigerator before serving.
    Calories: 220kcal | Carbohydrates: 33g | Protein: 4g | Fat: 9g | Saturated Fat: 1g | Polyunsaturated Fat: 3g | Monounsaturated Fat: 5g | Trans Fat: 1g | Cholesterol: 27mg | Sodium: 204mg | Potassium: 47mg | Fiber: 3g | Sugar: 18g | Vitamin A: 99IU | Vitamin C: 3mg | Calcium: 111mg | Iron: 1mg
    Tried this recipe?Mention @wellfedbaker or tag #wellfedbaker!
    Tiffany

    Tiffany is the recipe developer, stylist and food photographer behind Well Fed Baker. As a lifelong baker who had to go gluten free and dairy free in 2016, Tiffany strives to share allergen friendly recipes that never feel like they are free from anything.

    Reader Interactions

    Comments

    1. Savannah says

      May 17, 2026 at 7:44 pm

      Hey love! Going to make these but was wondering if the sugar could be swapped for honey? If so, what ratio would you suggest?

      Reply
      • Tiffany says

        May 18, 2026 at 12:35 pm

        Swapping sugar for honey can be tricky. I haven't tested this, so I can't promise it will work - but I would start with 1/4 cup of honey, reduce the milk to 5 tablespoons and reduce the temperature by 25 degrees. You may need to adjust the baking time by a couple of minutes.

        For reference, the swap is usually 1/2 cup of honey for every 1 cup of sugar. Reduce the liquid by 1/4 cup for every 1 cup of honey used. Lower the temperature by 25 degrees, because honey browns faster than sugar.

        Reply
    2. Christy Sample says

      February 03, 2022 at 9:24 pm

      5 stars
      Easy to make. Very flavorful.

      Reply
    5 from 4 votes (3 ratings without comment)

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    I love sharing gluten-free comfort food and homestyle baking, featuring Dutch oven meals, nostalgic dinners, classic baked goods, with dairy-free or allergen-friendly options. My recipes lean Southern, seasonal, and practical.

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