Whole Wheat Sourdough Muffins

Surprisingly light and soft, these whole wheat sourdough muffins are made using an overnight ferment for easier to digest, delicious muffins. Skip the long ferment and bake right away if you prefer.

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Ingredients You'll Need and Why

Start with the basics: whole wheat flour, brown sugar, eggs, milk, and butter. Vinegar adds lift, orange adds flavour, and a little starch makes the muffins much softer. These are our notes from recipe testing. You can find the full recipe card below with complete measurements and instructions.

• Whole wheat flour: this can be store-bought or home-milled, either way is great, but you should definitely weigh your ingredients if home-milling. We use standard whole wheat flour (not pastry flour) for this recipe. For a lighter muffin, try half whole wheat and half white flour. We often use a mix of white and whole wheat for extra flavour. See our cinnamon raisin sourdough and seeded sourdough bread, among others.
• Sourdough starter: this can be starter made with any type of flour (rye, wheat, spelt, etc.) and either active sourdough starter or sourdough discard.
• Milk: use full-fat dairy milk for the best flavour. Buttermilk can be substituted for the vinegar and milk mixture if preferred. If you do use buttermilk, don't forget to omit the vinegar from the recipe.
• Vinegar: apple cider vinegar, 5% white vinegar, or lemon juice in a pinch. This is used to make a homemade buttermilk alternative, which we prefer as many readers don't typically buy buttermilk - this way you're not left with an almost-full bottle of buttermilk that you're not sure how to use up.
• Starch: a small amount of added cornstarch to the recipe really lightens the muffins and makes them much softer. This imitates pastry flour without losing the structure and fibre from the whole wheat flour.
• Brown sugar: light or dark brown sugar, whatever you have on hand. We prefer light brown sugar but dark is good too.
• Butter: salted butter, melted and cooled. If you only have unsalted butter, add an extra pinch of salt to the dry ingredients. Olive oil can replace the butter if preferred.
• Orange: you're using the zest, so choose an unwaxed organic orange if possible and wash well before zesting.
• Egg: just one egg is enough - remember you're only making 8 muffins - and helps to bind the batter and provide extra rise.
• Vanilla: you might not notice the vanilla extract when it's there, but your muffins will taste flat if you leave it out! If you don't have vanilla, add another spice like cinnamon to help make up for it.
• Add-ins: try frozen berries (see sourdough blueberry muffins), seeds or chopped nuts, chocolate chips, and raisins or other dried fruit. Cinnamon and other spices like apple pie spice are excellent additions.
• Make it dairy-free: we recommend unsweetened soy milk and a good dairy-free butter alternative that comes in stick or block form, not in a tub.

How to Make Sourdough Muffins

This is a slightly different method compared to an average muffin recipe, and that's because of the whole wheat flour. You want to let the batter hydrate for at least 15 minutes before baking, but a long ferment is ideal for the best texture and taste.

I tested this recipe with a sponge starter, but it was an unnecessary complication that didn't result in better muffins. This method is more effective.

Step 1: mix the dry ingredients in a large mixing bowl and set aside. If the flour or cornstarch is lumpy, sift it through a fine mesh sieve rather than just whisking. I always sift baking powder and baking soda to remove lumps.

Step 2: mix the brown sugar and butter, then whisk in the egg, followed by the milk mixture, starter, vanilla, and orange zest. Make sure the milk and egg are both at room temperature.

Step 3: transfer the butter mixture to the dry ingredients and whisk until just combined. If you're worried about over-mixing, switch to a spatula instead of mixing entirely with a whisk. Over-mixing makes the muffins tough and dense.

Let the mixture rest for at least 15 minutes while the oven preheats, or refrigerate for up to 12 hours before baking. 1 hour is fine, 4 hours are fine.

Step 4: transfer the batter to a lined muffin tin, only filling 8 cups. The muffin cups should be filled right to the top but muffin tins do vary quite a bit in size.

Related: Sourdough Pumpkin Muffins

Step 5: bake at the higher temperature for 5 minutes before reducing the temperature and baking for another 12 to 15 minutes. Set a timer for both of these so that you don't forget to reduce the temperature.

Step 6: wait for the muffins to cool fully before serving. The texture is a little bread-like when still warm, and they can be gummy and slightly chewy before they cool.

Related: Whole Wheat Sourdough Bread

Expert Tips for the Best Muffins

• Cool before eating: this is especially true if you choose to the overnight ferment (for any sourdough muffins). The texture changes due to the fermentation, becoming more bread-like, and just like sourdough bread, can be very gummy when still warm. Let the muffins cool fully and they'll taste great.
• Fill the cups: this recipe will make enough batter to fill 8 standard muffin cups right to the top before baking. The muffins will rise into a nice tall dome without spilling over the edges when baking. It has been developed to make 8 muffins, not 12!
• Don't skip the hot bake: the muffins won't get the same rise and dome if they're baked at a steady temperature the whole time. For the best texture, be sure to bake at the high temperature for the first 5 minutes. You'll see this method used for a lot of muffin recipes, and it does make a big difference when eggs are included in the batter.
• Use newish starter: this isn't the time for ancient, grey discard that's been sitting at the back of the fridge for ages - use discard that's less than a week old, or use fresh starter or levain.

More Sourdough Discard Recipes