Blueberry Lemon Poppy Seed Sourdough Muffins Recipe
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These Blueberry Lemon Poppy Seed Sourdough Muffins are pulling out all the stops. Full of brightness from the freshly squeezed lemon juice, nuttiness from the poppy seeds, tartness from the blueberries, sweetness from the crumble topping, and a zip from the lemon glaze. If you love this flavor combo as much as I do, you’d also love my Sourdough Discard Lemon Blueberry Sweet Rolls!
It’s a bakery-style muffin with the goodness of sourdough. A perfect muffin to start your morning or to enjoy as a quick snack.

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Why You’ll Love This Recipe:
Delicious:
We can’t get enough of lemon and blueberries around here – just like my Lemon Blueberry Sourdough Bread, this recipe certainly pulls out all the stops. From the moist muffin to the buttery sweet crumble topping to the lemon glaze, how can it get better than that?
Great use of sourdough discard:
To make Blueberry Lemon Poppy Seed Sourdough Muffins you will need a cup of sourdough discard. It’s super helpful to have delicious recipes like this when you have a surplus of discard when you are making your own sourdough starter.
No-fuss recipe:
When I say these are easy lemon poppy seed muffins to make, I mean it! All you need are two bowls and a whisk for this recipe. Feel free to pull out a stand mixer or hand mixer, but it really isn’t necessary. This batter comes together with ease and makes for a simple clean-up afterward.

Ingredients You’ll Need
* To find precise measurements, scroll to the bottom of this post to find the recipe card*
Muffin Batter:
- All-purpose Flour – I used all-purpose flour for this recipe.
- Leaveners – For the best rise, double-check that your baking powder and baking soda haven’t expired! Otherwise, the muffins won’t rise.
- Lemons – If you want the best lemony flavor, I highly recommend using freshly squeezed lemon juice and zest over bottled.
- Sourdough Starter Discard – I prefer using fresh sourdough discard for sweet recipes, like these muffins. No older than 1-2 days. You can also substitute sourdough discard with active sourdough starter, just be sure to use the same amount in grams.
- Sour Cream – This can be substituted with Greek yogurt.
- Unsalted Butter – If all you have is salted butter, reduce the salt by 1 gram (1/4 teaspoon).
- Fresh Blueberries – You can use frozen blueberries as well. No need to thaw the blueberries before adding them to the batter.
Crumble Topping:
- Unsalted Butter – Use cold unsalted butter. I like to remove the butter from the fridge 5 minutes before for easy mixing. If you only have salted butter, omit the salt from the crumble topping.
Glaze Topping:
- Lemon Juice – Again, for the best lemon flavor, use freshly squeezed lemon juice over store-bought.
How to Make Blueberry Lemon Poppy Seed Sourdough Muffins:
Crumble Topping:
In a medium bowl, add white and brown sugar, flour, cinnamon, and cold, cubed butter.
Crumble the larger pieces of butter with your fingers and mix by hand until the butter is well coated with the flour mixture.

In a medium bowl, add white and brown sugar, flour, cinnamon, and cold, cubed butter.
Crumble the larger pieces of butter with your fingers and mix by hand until the butter is well coated with the flour mixture.
Batter:

- Sift flour, baking powder, and baking soda into a large bowl

- Add poppy seeds and salt to the dry ingredients and whisk until combined. Set to the side.

- In a large mixing bowl, add the sugar and fresh lemon zest. Rub the sugar and zest with clean hands until the sugar turns a pale yellow color. That way the sugar soaks in all the lemon oil.

- Next, add the sour cream, sourdough discard, melted butter, lemon juice, eggs, and vanilla, and mix until smooth.

- Pour the wet ingredients into the dry ingredients and whisk until the flour is just incorporated. The muffin batter will be quite thick.

- Lastly, fold in the fresh berries with a wooden spoon.
Bake:
Preheat the oven to 425 degrees F.
Grease your muffin tin or place paper liners in each spot. Divide batter between 24 muffin cups and sprinkle generously with the crumble.


Bake on the middle rack for 14-15 minutes, or until they are golden brown and a toothpick comes out with just a few crumbs.
Place the muffin pan on a cooling rack and leave the lemon muffins in for an additional 10 minutes
Remove and cool completely before topping with the sweet lemon glaze.
Glaze Topping:
In a separate bowl, mix fresh lemon juice with powdered sugar. Add more lemon juice until you reach your desired consistency.
Add the glaze to a piping or Ziploc bag, cut the corner, and drizzle on the lemon poppyseed muffins for an extra delicious lemon fresh flavor.

How to Serve:
Blueberry Lemon Poppy Seed Sourdough Muffins make for an excellent and quick morning breakfast with a hot cup of coffee. Or are a grab-and-go afternoon snack. The day after I’ve baked them, I like to pop them into the microwave just for 10 seconds or so to reheat. The glaze melts a bit and the blueberries get warm. It’s such a delight!

How to Store:
Blueberry Lemon Poppy Seed Sourdough Muffins will stay fresh when stored in an airtight container for up to 3 days.
FAQs
Absolutely! With the help of frozen blueberries, this sweet treat can be enjoyed all year long. No need to thaw your frozen blueberries before folding them into the batter. If you do, the blueberry juices may turn the batter purple. A fun presentation, but not a traditional, serving style.
I did make a batch of long-fermented blueberry lemon poppy seed muffins. I prepared the batter as described in the recipe, covered it, and placed it in the fridge to ferment for 24 hours. The end result had a beautiful rise, higher and more round than my quick version. But the crumb was a bit dense, not as light and airy as the ones made with discard and the sourdough flavor was more prominent. Technically not bad, but not my preference.
You can use bottled lemon juice made from concentrate if that’s what you have. It works well as a substitute for fresh lemon juice, although I personally think fresh lemons provide a brighter, more vibrant flavor.
Lemon extract is different from lemon juice and should not be used as a direct substitute. If you want to try it, use half lemon extract and half water to replace the amount of lemon juice called for.
So, for 2 tablespoons of lemon juice, use 1 tablespoon of lemon extract mixed with 1 tablespoon of water. I haven’t tested this version, but if you give it a go, let me know how it turns out!
Yes, you can use almond flour, whole wheat flour, or spelt flour, but each will change the texture and flavor in some way. Almond flour will make the muffins denser and moister. Your sourdough blueberry muffins may not rise as much since this flour type lacks gluten, so you might need to add more liquid.
Whole wheat flour will give the muffins a heartier flavor. It absorbs more moisture, so be sure to add extra liquid if needed.
Spelt flour is lighter than whole wheat and gives a mild, nutty flavor. It will still make soft muffins, but you may need to adjust the amount slightly. Start by swapping flour 1:1 and adjust based on how the batter looks and feels.

Sourdough Blueberry Lemon Poppy Seed Muffins Recipe
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Equipment
Ingredients
Crumble Topping:
- 55 grams brown sugar 1/4 cup
- 50 grams white sugar 1/4 cup
- 50 grams all-purpose flour 1/3 cup
- 1 gram cinnamon 1/2 teaspoon
- Pinch of salt
- 57 grams unsalted butter, cold 1/4 cup
Muffins:
- 330 grams all-purpose flour 2 1/4 cups
- 8 grams baking powder 2 teaspoons
- 3 grams baking soda 1/2 teaspoon
- 30 grams poppy seeds 3 Tablespoons
- 3 grams salt 1/2 teaspoon
- 200 grams sugar 1 cup
- 10 grams lemon zest 2 Tablespoons
- 250 grams sour cream, room temperature 1 cup
- 240 grams sourdough discard 1 cup
- 113 grams unsalted butter, melted 1/2 cup
- 75 grams lemon juice, freshly squeezed 1/3 cup
- 2 eggs
- 6 grams vanilla extract 1 1/2 teaspoons
- 200 grams fresh blueberries 1 1/2 cups
Lemon Glaze:
- 30 grams lemon juice, freshly squeezed 2 Tablespoons
- 120 grams powdered sugar 1 cup
Instructions
Crumble Topping:
- In a medium bowl, add white and brown sugar, flour, cinnamon, salt and cold, cubed butter.55 grams brown sugar, 50 grams white sugar, 50 grams all-purpose flour, 1 gram cinnamon, Pinch of salt, 57 grams unsalted butter, cold
- Crumble the larger pieces of butter with your fingers and mix by hand until the butter is well coated with the flour mixture.It’s best to work quickly in order to prevent the butter from getting too soft. Softened butter will melt during the baking and result in a flat crust, rather than a crunchy crumble.
- Place the bowl of crumble topping in the fridge to chill until ready to top the muffins.
Batter:
- Sift flour, baking powder, and baking soda into a large bowl. Add poppy seeds and salt to the dry ingredients and whisk until combined. Set to the side.330 grams all-purpose flour, 8 grams baking powder, 3 grams baking soda, 30 grams poppy seeds, 3 grams salt
- In a large mixing bowl, add the sugar and fresh lemon zest. Rub the sugar and zest with clean hands until the sugar turns a pale yellow color. That way the sugar soaks in all the lemon oil for a more citrusy flavor.200 grams sugar, 10 grams lemon zest
- Next, add the sour cream, sourdough discard, melted butter, lemon juice, eggs, and vanilla, and whisk until smooth. You can substitute the sourdough discard with active starter, just use the same amount in grams. For best results, use all room temperature ingredients.250 grams sour cream, room temperature, 240 grams sourdough discard, 113 grams unsalted butter, melted, 75 grams lemon juice, freshly squeezed, 2 eggs, 6 grams vanilla extract
- Pour the wet ingredients into the dry ingredients and whisk until the flour is just incorporated. Over mixing can lead to a tough crumb. The muffin batter will be quite thick.
- Lastly, fold in the fresh berries.200 grams fresh blueberries
- Long Ferment: To long ferment this batter, cover and place in the fridge for 24 hours. When ready to bake, continue with the recipe as normal. Since the batter is cold, you may need to add a few minutes to the bake time. Check at 14 minutes and continue to bake if necessary.
Bake:
- Preheat the oven to 425 degrees F and grease your muffin tin or place paper liners in each spot. Divide batter between 24 muffin cups and sprinkle generously with the crumble topping.
- Bake on the middle rack for 14-15 minutes, or until they are golden brown and a toothpick comes out with just a few crumbs.
- Place the muffin pan on a cooling rack and leave the lemon muffins in for an additional 10 minutes.
- Remove and cool completely before topping with the sweet lemon glaze.
Glaze Topping:
- In a separate bowl, mix fresh lemon juice with powdered sugar. Add more lemon juice until you reach your desired consistency.30 grams lemon juice, freshly squeezed, 120 grams powdered sugar
- Add the glaze to a piping or Ziploc bag, cut the corner, and drizzle on the lemon poppyseed muffins for an extra delicious lemon fresh flavor.
- Serve and enjoy!




This recipe is amazing! I love having the cup of discard in there. Have you tried to freeze these? We won’t go through all these muffins in 3 days but would love to have extra on hand in the freezer
Came together quickly and absolutely delicious!
Amazing! Thank you for sharing!
Yum!! Some of my absolute favorite flavors, and sourdough to boot 😋 thanks for sharing!
Oh my word! These look delicious! We love homemade muffins around here! I’ll have to try this recipe this weekend!
Thank you so much! I hope you and your family enjoy this delicious recipe 🙂
My pleasure! It’s the perfect balance of sweet and tart. Enjoy!
These look so yummy! I absolutely love blueberry muffins and that hint of lemon I’m sure adds a lovely zing! Will definitely be trying these in the near future!
You’re exactly right! It’s a great balance of sweet and tart. Enjoy 🙂