Side view of lemon poppy seed muffins in papers.

Truly Sourdough, Lemon Poppy Seed Sourdough Muffin Recipe

Most sourdough muffins simply use some discard in them, so I called these a “quickie sourdough.” While they use up some of the ever-present discard jar in my fridge…the flour in them is not truly fermented, so when one has a sensitive tummy, these don’t have the benefit of fermentation to keep that tummy happy.

This recipe is the best of both worlds, you can mix and bake right away when you are short on time, OR ferment part of the dough overnight (or all day) and then mix and bake to make the muffins a true sourdough.

Side view of lemon poppy seed muffins in papers.

While muffins are fun, when one is feeding many children…one can get tired of scooping and baking muffins. I’m happy to tell you that you can bake this recipe in a 9×13 pan, for just a few minutes longer, and then just slice and cut like a cake. 

You can bake the batter as is, or we like to dress up in two different ways. If you plan to freeze them, I do not suggest topping them, the toppings get soggy in the freezer.  One way is some organic cane sugar sprinkled on top before baking- it makes a lovely sweet crunch that makes this muffin skirt the line on a cupcake. Which is how I like my muffins…

Muffin batter baked into a 9x13 glass baking dish.

The other way is a quick lemon glaze after they come out of the oven, which works best on a 9×13 pan. If you planned to freeze it, you could take it out of the freezer, fully thaw and then top with a lemon glaze and be on your way!

Mixing up the dough does take a little elbow grease by hand, so feel free to use your mixer, but I find a Danish dough whisk makes short work of mixing by hand. They work well on any batter and are super easy cleaning – stuff doesn’t get stuck like it would in a regular whisk.

Top view of three lemon poppy seed muffins resting on a kitchen towel.

Baking in a casserole dish makes it easy for you to bulk bake and freeze for another day because muffins freeze so well! Definitely give it a try when your discard is starting to take over the fridge.

Side view of lemon poppy seed muffins in papers.
Print Recipe
4.82 from 11 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 9×13 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 9×13 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 9×13 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 9×13 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

Grab and Go Baking


  • Wendy

    I’m assuming that you would add the flour with the first ferment? I’m looking forward to trying them once I’ve woken up my sourdough starter.

  • Melinda

    So yummy! My family devoured this. For anyone interested, I substituted coconut sugar for the muffins, and I also made powdered sugar with coconut sugar. It turned out great!

  • Alison

    I just made these with GF starter and just random GF flours (sorghum, tapioca, arrowroot). 1. such an easy recipe (i didn’t sour them and literally dumped all the ingredients in a big bowl and used a hand mixer). 2. I appreciate that its a larger recipe, i think i’ll use this as the base for all my muffins from now on. Kate, I love every recipe of yours i’ve tried! Any of the regular ones so far have been easy for me to convert to GF (we have celiac). Thanks so much!

  • Heather_Cavinder

    Oh my this recipe is a keeper! My family devoured these so fast! Will definitely be adding to my breakfast rotation!!

  • Kendra

    5 stars
    I really had to trust the process while making these and I am so happy I did! They turned out amazing. Very flavourful and definitely a recipe to keep. Both my kids, even my super picky eater, LOVED these.

  • Emily

    5 stars
    This recipe is wonderful! I omitted the poppy seeds and added blueberries to make our Christmas morning muffins. It was flawless! It made 9 muffins and two loaf pans. I added cranberries to one of the loaf pans… SO good! This is now saved as my go to for Christmas morning!

  • christine knecht

    5 stars
    Two whole cups of sourdough discard!? You have outdone yourself haha. I just got done mixing, will let it ferment overnight, and I’m so excited for the end result. Thanks!

  • Blair

    I don’t have baking powder only baking soda so can I just use self rising flour instead of all purpose since it has those in it already? I’ve done that for other recipes but never for anything that involves sourdough as I’m new to making sourdough and learning what all I can make with it.


      Not sure on the self rising flour, but you can make baking powder using baking soda, cream of tartar and salt. I use the Joy of Cooking recipe for that.

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