Potato Flake Sourdough Lemon Poppy Seed Muffins

There’s something about the fresh, bright lemon flavor of potato flake sourdough lemon poppy seed muffins that just feels like spring—no matter the time of year. These muffins are soft, zesty, and lightly sweet with a satisfying crunch from the poppy seeds. But this isn’t your average lemon muffin recipe. We’re taking things up a notch with a fermented twist: potato flake sourdough discard.

If you’re maintaining a potato flake sourdough starter (like we do here at Little Tennessee Home), you know the joy of finding new ways to use your discard. Making muffins are one of my favorite ways to reduce waste, boost flavor, and sneak a little fermentation goodness into a sweet treat.

Let’s dive into the recipe, step-by-step. I’ll walk you through how to get that perfect balance of lemon flavor and tender texture—and show you how easy it is to work discard into your favorite bakes.

Tools You’ll Need

Before you get started, gather some basic kitchen tools to make the process smooth and stress-free. 

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• Large mixing bowl – For combining your ingredients and fermenting the batter.
• Zester or microplane – To get that fragrant lemon zest.
• Measuring cups and spoons – Accuracy counts for baking!
• Kitchen scale (optional) – Great for weighing the dry ingredients for consistent results.
• Rubber spatula – Gentle on your batter and perfect for folding in ingredients.
• Whisk – To mix wet ingredients until smooth.
• Standard muffin pan – This recipe makes about 12 muffins.
• Parchment muffin liners – Keeps cleanup easy and muffins from sticking.
• ¼ cup scoop – For evenly portioning out your muffin batter.
• Wire rack – For cooling your muffins before glazing.
• Small bowl and spoon or fork – For mixing and drizzling the lemon glaze.
• Quart Freezer bag-For piping glaze, if desired. 

Ingredients You’ll Need

For the muffins:

• 2 ½ cups all-purpose flour
• 1 cup raw organic sugar
• Fresh Lemon Zest of 2 lemons (about 8 grams)
• ½ cup melted coconut oil or butter (make sure it’s cooled—not hot)
• ½ cup potato flake sourdough discard (can also use active starter if that’s what you have on hand)
• 2 tablespoons poppy seeds
• 1 tablespoon fresh lemon juice
• 1 egg
• ¼ cup plain yogurt (can use greek yogurt, and also can use sour cream as a substitute)

After fermentation:

• 1 teaspoon baking soda
• 2 teaspoons baking powder
• ¼ teaspoon salt
• 1 teaspoon vanilla extract

For the lemon glaze:

• 1 cup powdered sugar
• 2 tablespoons lemon juice

The Flavor Secret: Lemon Sugar

To really amp up the fresh lemon flavor in these muffins, we start by creating a simple lemon sugar. Add your sugar to a mixing bowl, then grate in the zest of two fresh lemons. Use your fingers to rub the zest into the sugar until it becomes fragrant and tinted a soft yellow. 

This helps release the essential oils from the zest and infuses the sugar with bold citrus flavor.

Don’t toss those lemons just yet—you’ll juice them for both the muffin batter and the glaze.

Mixing the Batter

To the lemon sugar, whisk in the egg, yogurt, lemon juice, potato flake discard, and melted coconut oil (ensure it is not hot, or this will kill your starter). 

Next, stir in the flour with a rubber spatula until just combined. The batter will be thick. Cover the bowl tightly with plastic wrap or a reusable cover and set it aside at room temperature for fermentation.

This long rest helps the flour absorb moisture, the ingredients to become more digestible, and bring subtle flavor complexity to the final muffins. I recommend fermenting for at least 8 hours and up to 16. You can mix it up in the evening and bake fresh muffins in the morning—perfect for lazy weekends or brunch with guests.

Baking Time

Once your batter has fermented, it’s time to transform it into beautiful muffins.

Preheat your oven to 400°F with the rack in the center position. While the oven preheats, line a standard muffin tin with parchment paper liners (or grease them well if you’re not using liners).

Add the remaining ingredients—baking soda, baking powder, salt, vanilla, and poppy seeds—to the fermented batter. Stir everything together gently but thoroughly. 

Scoop the batter into the muffin cups using a ¼-cup measuring scoop or cookie scoop. Fill each cup about ¾ full.

Place the pan into the hot oven and immediately reduce the temperature to 375°F. This little trick helps give the muffins a nice domed top. Bake for about 18–22 minutes, or until the tops are golden and a toothpick inserted into the center comes out clean.

The Perfect Glaze

While the muffins are cooling, whisk together your powdered sugar and lemon juice to make a tangy glaze. The consistency should be thick but pourable—like maple syrup. If it’s too thick, add a tiny splash of lemon juice at a time.

Once the muffins have cooled for about 10 minutes, drizzle the glaze over the tops. Let it set for a few minutes, then serve warm or at room temperature.

Tips for Success

• Don’t skip the lemon sugar step! It’s a small touch that makes a big difference in the flavor.
• Moist Muffins:  To make sure that your lemon muffins are moist, the yogurt or sour cream is the key!
• Make it dairy-free. Use coconut oil and a dairy-free yogurt if needed. These muffins are easily adaptable.
• Want extra crunchy poppy seeds? Go for it! Two tablespoons give a nice crunch, but you can add up to three if you really love the texture.

Storing & Freezing

These potato flake sourdough lemon poppy seed muffins keep beautifully at room temperature in an airtight container for up to 3 days. For longer storage, pop them in the freezer (unglazed) for up to 2 months. Just thaw and drizzle with fresh glaze before serving.

Pin for later and Share with a friend: 

These lemon poppy seed muffins have become a favorite in our home—especially when I want something a little special but still homemade and simple. The addition of potato flake sourdough discard gives them an extra depth that you just don’t get in traditional muffin recipes.

Whether you’re baking to use up discard or just craving something bright and sunny, I hope you enjoy this recipe.

Have questions about potato flake sourdough discard or fermenting baked goods? Leave a comment below or send me a message—I’m always happy to help! You might also enjoy following along on facebook for tips, tricks and updates!

If you give this recipe a try, I would greatly appreciate if you came back and gave it a 5-star review! It helps me out so much! 

I also love seeing all of the delicious creations you make! Share your photo over on instagram and give me a tag @littletennesseehome