Sourdough Lemon Poppy Seed Muffins

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Soft, bakery-style sourdough lemon poppy seed muffins are made with sourdough discard for added depth of flavor and moisture, and finished with a sweet lemon glaze.

Sourdough lemon poppy seed muffins on a serving plate.

These muffins strike the balance between light and tender while still feeling substantial. The combination of lemon zest and juice gives a clean, fresh citrus flavor, while the sourdough discard adds subtle complexity without overpowering the recipe.

The batter comes together easily and bakes into nicely domed muffins with a soft crumb. A simple lemon glaze takes these to the next level.

For more sourdough lemon recipes, try this Lemon Blueberry Sourdough Bread, Sourdough Lemon Bars, Sourdough Lemon Bread, and Sourdough Lemon Poppy Seed Scones.

Why You’ll Love Sourdough Lemon Poppy Seed Muffins

Fresh Lemon Flavor: With fresh lemon juice and zest, these muffins are loaded with lemon flavor.
Uses Discard: When you have extra sourdough discard you want to use up, these delicious muffins are a great way to use it.
Great for Breakfast or Snacks: Sourdough discard recipes like my sourdough granola, sourdough granola bars, and sourdough pop tarts are perfect for breakfast or snacks. These lemon poppy seed sourdough muffins are another recipe to add to your list of easy breakfasts and snacks. But they also look special enough to add to a brunch table.

Ingredients

Find the full list of ingredients, amounts, and instructions in the printable recipe card at the bottom of this post.

Flour: I usually use unbleached all-purpose flour.
Baking Soda and Baking Powder: These are the leavening agents in this discard recipe.
Sugar: White granulated sugar is the sweetener.
Sourdough Starter: You’ll need a sourdough starter for this recipe. Here’s how to make your own sourdough starter. You can use sourdough discard or active starter.
Butter: Unsalted butter is used. If you only have salted butter, you may want to reduce the salt in the recipe.
Poppy Seeds: Crunchy poppy seeds add so much to this recipe.
Lemons: This recipe uses fresh lemons for their zest and juice.
Greek Yogurt or Sour Cream: Do not use protein enhanced greek yogurt, as the additional protein compounds added to this type of yogurt will dry out your muffins.
Vanilla: You can use either store-bought vanilla or homemade vanilla extract.

How to Make Sourdough Lemon Poppy Seed Muffins

Here are the step-by-step instructions for making these sourdough lemon poppyseed muffins:

Step 1: Preheat the oven to 425°F (220°C). Line a 12-cup muffin tin with liners (or grease the muffin cups).

In a bowl, whisk together flour, baking powder, baking soda, salt, and poppy seeds.

Step 2: In a separate bowl, rub the fresh lemon zest into the sugar until fragrant. Add the melted butter and whisk until fully combined. Add the eggs and whisk until smooth and slightly thickened 30-60 seconds.

Mix in the sourdough discard, yogurt, milk, lemon juice, and vanilla extract until fully combined.

Step 3: Add the dry ingredients to the wet ingredients and gently mix just until no dry streaks remain. Do not overmix.

Step 4: Let the batter rest for 10–15 minutes to allow the flour to hydrate and improve structure.

Collage of four photos showing steps 5-8 for how to make sourdough lemon poppy seed muffins.

Step 5: Divide the batter evenly, filling each of the paper liners to the top and slightly mounding the centers.

Step 6: Bake at 425°F for 7 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 12–16 minutes, until the tops are golden and domed and the centers are set.

Allow muffins to cool slightly on a wire rack.

Step 7: Whisk glaze ingredients until smooth.

Step 8: Drizzle over warm or cooled muffins. Sprinkle tops with lemon zest and/or extra poppy seeds if desired.

Spoon drizzling lemon glaze on sourdough lemon poppy seed muffins.

Sourdough lemon poppy seed muffins on a wire rack.

How to Store

Store leftover muffins in an airtight container at room temperature for up to 2 days, or refrigerate for up to 4 days. The glaze may melt into the muffins over time.

How to Freeze

Freeze unglazed muffins for best results. Thaw at room temperature and add glaze before serving.

Sourdough lemon poppy seed muffins in a stack on a plate.

Recipe Tips

The muffin batter should be thick enough to hold a slight mound when scooped. If it feels too loose, it may result in flatter muffins.
The initial high oven temperature helps create a strong rise and domed tops.
Resting the batter improves texture and helps the muffins bake taller.
Do not overbake. The muffins should be set but still soft in the center for a tender crumb.