Want something satisfying but loaded with fiber and sourdough goodness? These sourdough flax seed muffins are perfectly sweet, dotted with berries, and topped with a crumble that will have you reaching for another!

I’m a bit of a crunchy mom, and love making homemade foods that help us all feel our best. The idea for these delicious muffins was inspired as I was looking for ways to add more fiber to our breakfast!
I use fresh ground whole grain flour but you can also use all purpose. Sourdough gives these muffins that depth of flavor that we all love, and it’s sweetened with a little pure cane sugar and a delightful crumble topping.
These sourdough falx seed muffins can be made long fermented or baked right away. If you are going to long ferment them, just wait to add the baking soda till after the bulk ferment;)

Simple Ingredients
Just a few simple ingredients make up these scrumptious muffins, including: flour, sourdough starter, sugar, salt, eggs, baking soda, vanilla extract, ground flax seed, apple sauce, avocado oil and frozen berries.
The simple crumb topping adds a nice tough of sweetness and texture. It’s made with just a few tablespoons of butter, flour, sugar and cinnamon. (I use cranberries, but frozen raspberries, or blueberries would also be delicious!)

Tips for Sourdough Flax Seed Muffins
Sourdough Starter Activity: Ensure your starter is bubbly and active before using it. If it’s not, feed it with equal parts flour and water and let it rise again.
Add-ins: Get creative with add-ins! Try chopped nuts, seeds (chia, sunflower), diced apples, blueberries, or grated zucchini.
Overmixing: Overmixing can lead to tough muffins. Mix just until combined.
Baking Time: Oven temperatures can vary. Start checking for doneness around 25 minutes and adjust baking time accordingly. A toothpick inserted into the center should come out clean.
Recipe Card
I hope you try these sourdough flax seed muffins. If you do, I’d really appreciate a review on the recipe card or tell me what you think, or any variations you made in the comments below!

Sourdough Flax Seed Muffins
Equipment
- 2 muffin tin pans
- 1 large mixing bowl
- 1 wooden spoon
- 18 paper muffin tin liners
Ingredients
For the Muffins
- 1 3/4 cup flour I use whole wheat einkorn, but all purpose works too
- 3/4 cup granulated sugar pure cane sugar
- 3/4 cup flax seed ground
- 1 teaspoon salt
- 2 teaspoons baking soda if long fermenting, don't add this till done fermenting.
- 1/2 cup sourdough starter active
- 2 eggs large
- 1/2 cup applesauce
- 1/2 cup oil avocado oil or olive oil
- 2 cups berries frozen, cranberries, raspberries or blueberries
For the Crumble Topping
- 1/2 cup granulated sugar
- 1/3 cup flour
- 1/4 cup butter cold, and cubed
- 1 1/2 teaspoons cinnamon ground
Instructions
- Preheat your oven to 350 degrees F.
- Add dry ingredients to a large mixing bowl: flour, ground flax seeds, salt, sugar (if baking right away add baking soda. if long fermenting add the soda after fermenting)
- Use a whisk or a wooden spoon to mix dry ingredients till well combined. Then make a well in the center of the dry ingredients.
- To the flour mixture well add the wet ingredients: sourdough starter, eggs, oil, applesauce, and stir just till all the ingredients are combined into a thick batter. (If you are long fermenting, cover this bowl of batter with plastic wrap, and place in the fridge for at least 4 hours to overnight, then remove and stir in the baking soda.)
- Fold the berries into the thick batter till evenly mixed in. Do not over mix, it can lead to a tougher texture.
- Line 18 muffin tin cups with paper liners, or you can also just butter the inside of the muffin tins really well.
- Fill muffin tin cup 3/4 the way full. It will be thick, and that's the way it should be… Don't worry it will settle into the muffin tin as it bakes;)
- Make the crumble topping: in a smaller mixing bowl add: 1/4 cup cold cubed butter, 1/2 cup granulated sugar, 1/3 cup flour, and 1 1/2 teaspoons ground cinnamon. Use an electric mixer or a pastry cutter to cut the butter into the dry ingredients till it forms crumbles.
- Sprinkle about 2 teaspoons of the crumble topping over each muffin,
- Bake in preheated oven at 350 degrees F for 25-30 minutes… JUST till a toothpick inserted in the middle comes out clean. Do not overbake.
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