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Side view of lemon poppy seed muffins in papers.
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4.8 from 5 votes

Lemon Poppy Seed Sourdough Muffins

Whether you use discard or let the batter truly ferment, these sourdough muffins fit your schedule. Did you know you can bake muffins in a cake pan?
Prep Time10 mins
Cook Time20 mins
Fermenting6 hrs
Total Time6 hrs 30 mins
Course: Breakfast, Snack
Cuisine: American
Servings: 36 muffins
Calories: 235kcal


  • 1 1/2 cups sugar OR 3/4 cup honey
  • 1 cup buttermilk or milk kefir*
  • 2 cups sourdough starter discard
  • 3 cups flour all-purpose, whole wheat, or a mix
  • 2 tsp vanilla
  • 1/4 cup lemon juice
  • 1 tbsp lemon zest optional but terrific
  • 2 tbsp poppy seeds
  • 2 large eggs
  • 1/2 cup melted butter or liquid oil such as olive or sunflower oil
  • 1 tsp salt
  • 1 tsp baking soda
  • 2 tsp baking powder

Glaze (optional)

  • 1 1/2 cups powdered sugar
  • 1 tbsp vanilla
  • 2 tbsp lemon juice
  • 1-2 tbsp water to desired consistency


To ferment ahead of time for true sourdough:

  • Mix sugar, flour, buttermilk and sourdough discard together in a bowl. Cover and let sit on the counter 6 hours, up to overnight.

To make now:

  • Mix the sugar, flour, buttermilk and sourdough discard up and then immediately move onto the next step.
  • When ready to bake, preheat the oven to 350F. Mix in the vanilla, lemon juice, lemon zest, poppy seeds, eggs, melted butter, and salt. Mix well. Its going to be a little gloppy/hard to mix, but use your elbow grease!
  • Sprinkle the baking soda and baking powder over the whole dough, and mix well for 10-20 seconds. Let sit while you line your muffin pans or grease your 9x13 pan. The chemical reaction with the sourdough and the baking powder/baking soda with change the consistency of the dough to be more like a normal muffin batter.
  • Scoop 1/4 cup scoops into muffin papers/greased muffin pans or pour the whole bowl in a 9x13 pan.
  • If desired, sprinkle with coarse sugar such as organic cane sugar, maybe 1/2-1 tsp per muffin.

To bake:

  • Muffin tins take 20 minutes, turning halfway. Check with knife to make sure they are done
  • A 9x13 pan takes 30-35 minutes, turning halfway, check with a knife to make sure it is done.

To glaze:

  • 1 1/2 cups powdered sugar, 1 tbsp vanilla, 2 tbsp lemon juice and then if you want it thinner, 1-2 tbsp water. Pour over the 9x13 pan.


*You can also ‘water’ down plain yogurt to make it buttermilk consistency, roughly half plain yogurt with half milk or water.
These muffins/loaf really need to cool down to being just warm. If you eat them when they're still hot, they will stick to the papers and be gummy. Sourdough needs to cool down a bit to set up its ‘crumb structure.’
Nutrition is calculated without glaze.


Serving: 1muffin | Calories: 235kcal | Carbohydrates: 39g | Protein: 4g | Fat: 7g | Saturated Fat: 4g | Cholesterol: 36mg | Sodium: 314mg | Potassium: 59mg | Fiber: 1g | Sugar: 18g | Vitamin A: 210IU | Vitamin C: 2mg | Calcium: 64mg | Iron: 1mg