Tangy and zesty sourdough lemon poppy seed muffins bursting with fresh lemon flavor and a hint of nutty sweetness from the poppyseeds. These muffins are sure to make your taste buds dance with delight.

10 sourdough lemon poppy seed muffins with a lemon drizzle on a wire rack over parchment paper with a lemon sliced in half in the background

These flavorful muffins are surprisingly easy to make, perfect for a lazy Sunday morning brunch or a tasty afternoon snack.

The crunchy poppyseed topping adds a satisfying texture and a sweet, nutty flavor, while the light and airy texture of the muffin itself comes from whisking together the wet and dry ingredients separately. 

I love making muffins for breakfast or snacks. Start them the night before, let them ferment overnight, and then bake them in the morning. Warm homemade muffins first thing in the morning. No one will complain, I promise.

So grab your apron and a bowl, and let the fun begin as you create a batch of delicious and unique sourdough lemon poppyseed muffins.

close up of a lemon poppy seed muffin with a lemon glaze on a wire rack over parchment paper with two halves of a lemon in the background

Why you will love this recipe:

Great way to use extra sourdough discard. Especially if you are just getting started with sourdough recipes and are still in the thick of the frequent feedings.

Can be long fermented for better digestion and nutrition. Not only are fermented grains easier to digest but the phytic acid is also broken down during the process making the nutrients available in the grains more bioavailable for your body to absorb.

Delicious muffins. Yummy burst of fresh lemon flavor and crunchy poppy seeds with a sweet glaze.

sourdough lemon poppyseed muffin sliced in half of a wire rack. Another muffin and a half of a lemon are in the background

Tips:

  • These sourdough muffins can be made quick or long fermented.
  • The lemon drizzle over top adds the more delicious sweet flavor. You can totally opt out if you want, but it is so good.
  • If you are opting for the dairy free version using water and oil, I would suggest using a touch less oil. I tested it and they were absolutely delicious. More like cake, but on the moist side.

This post contains affiliate links, which means I make a small commission at no extra cost to you. See my full disclosure here.

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Tools you may need:

Stand mixer with paddle attachment, a mixing bowl with a hand mixer, or just a whisk will work. I suggest using a stand mixer if you are going to long ferment the muffin batter.

Muffin tin

Measuring cup

Ice cream scoop: This is totally optional, but it makes scooping the muffin batter into the muffin pan super simple and perfectly even.

Muffin liners

Kitchen scale (if wanting to measure in grams)

flour water and sourdough starter in a bowl with containers of ingredients surrounding the bowl

Ingredients

All purpose flour

Baking powder and Baking soda – This is what gives the muffins their rise.

Poppy seeds

Sugar 

Salt 

Wet Ingredients:

Sourdough starter discard – You could also use an active sourdough starter if that is what you have on hand. If using the quick version, active starter will not give you a tangy of a flavor.

Milk – You can also use water for a dairy free version.

Unsalted butter – For a dairy free version, you could swap the butter out for melted coconut oil, avocado oil, or even olive oil. 

Eggs

Fresh lemon juice – This adds the most delicious fresh lemon flavor. If you are in a pinch bottled lemon juice will also work. I just find fresh lemons to taste better.

Vanilla extractHomemade or store-bought

Lemon Glaze

Powdered sugar
Fresh lemon juice

ten lemon poppy seed sourdough muffins with a lemon glaze drizzled over top on a wire rack with two lemons and a large bowling the background

How To Make Sourdough Lemon Poppyseed Muffins – Quick Version

Preheat your oven to 400 F and prepare your muffin tins. You can either use paper liners, or grease them with cooking spray or coconut oil rubbed inside each tin.

In a large bowl, combine the flour, baking powder, baking soda, poppy seeds, sugar and salt.

In a medium bowl, whisk together the sourdough starter, milk, melted butter, eggs, lemon juice and vanilla until well incorporated.

Slowly add the dry ingredients to the starter mixture and gently combine. Be careful not to over mix.

Spoon the batter into the prepared muffin tins.

Bake for 20 minutes, or until a toothpick (or cake tester) inserted in the middle comes out clean. The edges of the sourdough lemon poppy seed muffins should start to turn golden brown.

Remove to a wire rack to cool.

lemon drizzle in a stone bowl with a whisk and muffins to the right

For the glaze, whisk the powdered sugar and lemon juice in a small bowl until combined. You can either drizzle it over the top with a spoon, or add it to a piping bag. I use a ziplock bag with the corner clipped off.

Enjoy!

Long Ferment Option 1 

This is what I typically do, and the muffins in the photos were made this way with a 12 hour ferment.

sourdough starter, milk, and flour in a large bowl with a wooden spatula

The night before, add the all purpose flour, sourdough starter, and milk to a bowl and combine. 

Cover with plastic wrap, a tight lid, or a beeswax wrap. Allow to sit at room temperature for 8-12 hours.

long fermented sourdough lemon poppyseed muffin batter in a large bowl with a wooden spatula with a muffin pan to the right and sliced lemons to the left

The next day, preheat oven to 400 degrees.

Add in the baking powder, baking soda, sugar, salt, butter, eggs, lemon juice and vanilla to the fermented batter.

Bake for 20 minutes, or until a toothpick inserted in the middle comes out clean.

Remove to a wire rack to cool.

Note: if you are uncomfortable with leaving out milk overnight, you could substitute with water.

three sourdough lemon poppy seed muffins on a wire rack with two lemon halves in the background

Long Ferment Option 2

I am comfortable allowing the milk to sit out for a lengthy period of time, but this is milk from our farm that we trust. Use discretion here. If you prefer to ferment in the refrigerator, you can mix up the entire batter with all of the ingredients from the original instructions, and put it covered in the fridge for 12 hours or up to 2 days

Storage: 

Store in an airtight container at room temperature for 5-7 days. Freeze for longer term storage.

6 lemon poppy seed sourdough muffins on a wire rack with lemon halves and a bowl in the background

FAQ:

Why bake with sourdough discard?

One, it is an easy way to use up any extra sourdough discard you may have. Also, it adds a delicious tangy flavor and can be long fermented for health benefits.

What can you do with sourdough discard?

You can use sourdough discards in so many ways. From pizza, to english muffins, to pancakes, bread and more. Check out these 35+ sourdough recipes.

What does sourdough do in baking?

Sourdough starters can be used to provide subtle flavor, texture, and leavening to baked goods. Bakers use the starter to make a variety of breads, including pizza crusts, sandwich breads, focaccia, and flatbreads. The sourdough starter not only adds flavor to the end product, it also improves the digestibility of the baked goods. With its versatility and high nutrient content, sourdough is an ideal baking ingredient for creating unique and delicious recipes.

Find More Sourdough Muffin Recipes:

If you try this recipe and love it, I would love if you could come back and give it 5 stars! Tag me on Instagram @farmhouseonboone

Sourdough Lemon Poppy Seed Muffins

4.41 from 111 votes
Tangy and zesty sourdough lemon poppy seed muffins bursting with fresh lemon flavor and a hint of nutty sweetness from the poppyseeds.
Prep: 10 minutes
Cook: 20 minutes
Additional Time: 12 hours
Total: 12 hours 30 minutes
Servings: 12 muffins
ten lemon poppy seed sourdough muffins with a lemon glaze drizzled over top on a wire rack with two lemons and a large bowling the background
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Ingredients 

  • 2 cups all purpose flour, 280 grams
  • 2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 2 tablespoons poppy seeds
  • 1 cup sugar, 200 grams
  • 1/2 teaspoon salt, 2 grams
  • 1/2 cup sourdough discard, 142 grams
  • 1 cup milk, 236 grams
  • 1/2 cup unsalted butter, melted (120 grams)
  • 2 large eggs
  • 1 tablespoon fresh lemon juice
  • 1 teaspoon vanilla

Glaze

  • 1 cup powdered sugar, 113 grams
  • 2 tablespoons fresh lemon juice

Instructions 

Quick Version:

  • Preheat your oven to 400 F and prepare your muffin tins. You can either use paper liners, or grease them with cooking spray or coconut oil rubbed inside each tin.
  • In a large bowl, combine the flour, baking powder, baking soda, poppy seeds, sugar and salt.
  • In a medium bowl, whisk together the sourdough starter, milk, melted butter, eggs, lemon juice and vanilla until well incorporated.
  • Slowly add the dry ingredients to the starter mixture and gently combine. Be careful not to over mix.
  • Spoon the batter into the prepared muffin tins.
  • Bake for 20 minutes, or until a toothpick (or cake tester) inserted in the middle comes out clean. The edges of the sourdough lemon poppy seed muffins should start to turn golden brown.
  • Remove to a wire rack to cool.
  • For the glaze, whisk the powdered sugar and lemon juice in a small bowl until combined. You can either drizzle it over the top with a spoon, or add it to a piping bag. I use a ziplock bag with the corner clipped off.
  • Enjoy!

Long Ferment Option 1:

  • This is what I typically do, and the muffins in the photos were made this way with a 12 hour ferment.
  • The night before, add the all purpose flour, sourdough starter, and milk to a bowl and combine.
  • Cover with plastic wrap, a tight lid, or a beeswax wrap. Allow to sit at room temperature for 8-12 hours.
  • The next day, add in the baking powder, baking soda, sugar, salt, butter, eggs, lemon juice and vanilla.

Long Ferment Option 2:

  • I am comfortable allowing the milk to sit out for a lengthy period of time, but this is milk from our farm that we trust. Use discretion here. If you prefer to ferment in the refrigerator, you can mix up the entire batter with all of the ingredients from the original instructions, and put it covered in the fridge for 12 hours or up to 2 days

Notes

  • Note: if you are uncomfortable with leaving out milk overnight, you could substitute with water.

Nutrition

Calories: 290kcal | Carbohydrates: 46g | Protein: 5g | Fat: 10g | Saturated Fat: 6g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 0.3g | Cholesterol: 54mg | Sodium: 235mg | Potassium: 82mg | Fiber: 1g | Sugar: 28g | Vitamin A: 315IU | Vitamin C: 1mg | Calcium: 96mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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4.41 from 111 votes (100 ratings without comment)

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70 Comments

  1. Kristie says:

    5 stars
    These are a hit! I made them using the long refrigeration ferment process. I also used freshly milled whole wheat flour. They turned out great! I ate one prior to adding the icing and they were good, but the icing took them to the next level. Next time I might play with using something else in place of the sugar but I will definitely be making them again.

  2. Stefanie Lewis says:

    3 stars
    So Iโ€™m not sure what happened but I had a feeling 20 min at 400ยฐ would be too hot and I was right. Iโ€™ll try again at a lower temp. I love all FHOB recipes so Iโ€™m not giving up!

    1. Missy says:

      My thoughts EXACTLY! At 400*, mine were burnt when I checked them a little early at 18 minutes (and Iโ€™d even made a double batch!). Most muffin recipes bake at 350*, and I shouldโ€™ve went with my intuition. Also, I think Iโ€™ll add a little lemon zest next time I try these to bring out the flavor more.

  3. Mirtha Durand says:

    Can I make Mirtthis recipe and put the dough in a loaf pan? I’ve tried many of your recipes and all were really succesfull. Thanks

    1. Leslie says:

      4 stars
      Made these, but didn’t taste any lemon in the muffin. Good flavor though. I think I will put some zest in the next batch. Had some leftover and made a small loaf out of. Came out nice.

  4. Anna says:

    4 stars
    Made these for an Easter brunch! I read through the reviews ahead of time and went ahead and added extra lemon juice and lemon zest. I was glad I did–definitely helped the lemon flavor pop. I added 2 TBS of lemon juice–but probably could’ve done 3 or just the whole lemon. I also did 3/4 cup of sugar and it was plenty sweet enough.
    I did the overnight ferment with water because of dairy issues. They turned out yummy–a little tough and hard to get out of the muffin tin…not sure why.

  5. Haley says:

    5 stars
    These are amazing! The first muffin recipe I have made that didn’t come out too dry or crumbly. I did the colder ferment method and love that I am getting the extra health benefit.

  6. Katherine Pfeiffer says:

    5 stars
    Such a delicious recipe! I totally forgot about it as I long fermented it on the counter for 2 days, and then kept it in the fridge for another 6-7 days. I took it out this morning, added the remaining ingredients, and cooked it as a loaf. It was wonderful! I baked it at 350 for around 60-70 minutes.

    1. Lisa Bass says:

      Glad to hear it!

  7. Brenda K says:

    Lisa, thank you for this recipe! I just made the quick version this morning (I didn’t do prep last night…), baked a double batch in a 9×13 glass pan at 350* F for 35 minutes, drizzled the lemon glaze on each piece, and served it steaming hot. My family was tickled to be eating cake for breakfast, and it was delicious!

    1. Lisa Bass says:

      Sounds delicious.

  8. Nancy B says:

    I was out of butter so I substituted 1/4 cup oil and 1/4 cup applesauce. Still turned out great, very moist and I also added some lemon zest to the icing.

    1. Lisa Bass says:

      Ohhh that is an interesting substitution! Sounds yummy.

      1. BB says:

        Ever make these withe fresh milled whole grain? How much flour worked?

  9. Lora says:

    Thank you for sharing! These turned out great. I decreased the sugar to 150 grams, added lemon zest to the batter and fermented in the fridge over night. Turned out fabulous!

    1. Lisa Bass says:

      I love that! Glad you enjoyed the recipe.

  10. Rachel says:

    So delicious! I ended up using a mini muffin tin and it made about 55. I used the cold ferment method and the inside of the muffins are so moist and fluffy.
    If you donโ€™t put the glaze on, I recommend adding a tad more lemon into the batter.

    1. Lisa Bass says:

      Great tip! Glad you enjoyed the muffins.