Whole Wheat Sourdough Chocolate Chip Muffins With Fresh Milled Grains

You need to try these soft, delicious whole wheat sourdough chocolate chip muffins made with freshly milled flour. A perfect combination of tangy and sweet with the added nutritional benefits of whole grains.

Whole wheat sourdough chocolate chip muffins with a bite taken out on a plate with chocolate chips surrounding the muffin.

Muffins are one of my favorite things to bake (like these blueberry muffin or turn this sourdough banana bread into muffins).

They are easy to make, can be made in really large batches (which is perfect when you have a large family like mine), are delicious, they store well, and no one in my family ever complains about a muffin (which is huge).

If you love the unique flavor and texture of sourdough, these sourdough chocolate chip muffins will quickly become a new favorite. Made with freshly milled white wheat flour, these muffins bring together the tang of sourdough with the sweetness of chocolate chips in a light, fluffy texture.

Freshly milled flour adds a nutty, whole-grain flavor that enhances the muffins while boosting their nutritional value. This recipe is perfect for breakfast, a snack, or even as a dessert!

If you are new to milling grains, make sure to check out my post on how to mill flour at home.

Why You’ll Love This Recipe

Healthier: Freshly milled wheat is not only full of fiber, but it also packed with b vitamins, vitamin e, folate, and more.

Easy: This recipe is super easy to make. No weird ingredients

Make ahead snack or breakfast: I love making double or triple batches and then freezing them for later. Anytime someone wants a muffin, they can grab it from the freezer and pop it into the oven to warm.

Ingredients Needed

eggs, butter, flour, sourdough starter, and other ingredients on a countertop.

Sourdough starter – active sourdough starter or discard will work.

Freshly milled soft white wheat flour – you can substitute with store-bought whole wheat flourall-purpose flour with modifications if needed.

Unsalted butter – oil would also work.

Milk: or water

Chocolate chips (semi-sweet or milk chocolate, based on preference

A full ingredient list with exact amounts can be found in the recipe card below.

Tools You’ll Need

Grain mill: I have the Mockmill 200. Find my post all about the best grain mills.

Stand mixer (optional)

Muffin tin

How to Make Sourdough Chocolate Chip Muffins with Freshly Milled Flour

eggs, sugar, butter, and sourdough starter in a stand mixer bowl.

Step 1: Preheat your oven to 375°F (190°C). Line a muffin tin with muffin liners or lightly grease it to prevent sticking. In a large mixing bowl or the bowl of stand mixer, whisk together the sourdough starter, eggs, sugar, melted butter, and vanilla extract.

Adding dry ingredients to wet ingredients in a stand mixer.

Step 2: In another bowl, whisk together the freshly milled white wheat flour, salt, baking powder, and baking soda. Gradually add the dry mixture into the wet ingredients, stirring gently as you go. If it’s too thick, add a tablespoon of milk at a time to adjust the consistency

Adding chocolate chips to muffin batter.

Step 3: Once your batter is mixed, fold in the chocolate chips. Be careful not to overmix, as this could result in dense muffins.

Step 4: Spoon the batter into the muffin tin, filling each cup about 2/3 full. This ensures the muffins have room to rise without overflowing. I like to use an ice cream scoop.

Baked whole wheat sourdough chocolate chip muffins in a muffin pan.

Step 5: Place the muffin tin in the oven and bake for 18–22 minutes or until a toothpick inserted into the center comes out clean. The tops should be lightly golden brown.

Storage

Whole wheat sourdough chocolate chip muffin on a plate surrounded by chocolate chips with more muffins in the background.

Freshly baked sourdough chocolate chip muffins are best enjoyed within 2–3 days, but you can store them for up to a week in an airtight container at room temperature.

For longer storage, place them in the fridge for up to a week, or freeze them for up to 3 months.

To reheat, pop them in the microwave for a few seconds or warm them in the oven at 300°F (150°C) for about 10 minutes.

Tips for Success

Active starter or sourdough discard. Either will work since this recipe uses chemical leaveners.
Milling your own white wheat flour ensures your muffins are packed with flavor and nutrients. If you’re using store-bought flour, you may need to adjust the amount of liquid in the recipe since freshly milled flour tends to absorb more moisture.
Over-mixing the batter will lead to dense muffins. Stir until just combined for light, fluffy results.
Start checking your muffins at 18 minutes to avoid overbaking. All ovens are different, so the baking time can vary.

Variations

Nutty Muffins: Add 1/2 cup of chopped nuts, such as walnuts or pecans, to the batter for a crunchy texture.
Spiced Sourdough Muffins: Add 1 tsp of cinnamon and 1/2 tsp of nutmeg to the dry ingredients for a warm, spiced flavor.
Double Chocolate Chip Muffins: For an extra chocolatey treat, use a combination of cocoa powder and chocolate chips in the batter.
Fruit and Chocolate: Mix in 1/2 cup of dried fruit like raisins, cranberries, or chopped bananas along with the chocolate chips for a fruity twist.

FAQ

Can I use store-bought whole wheat flour instead of white wheat flour?

Yes! You can use store-bought whole wheat flour, but keep in mind that it may result in denser muffins. If using whole wheat, you might want to add a bit more milk or water to balance the texture.

How do I make this recipe dairy-free?

You can substitute the butter with coconut oil or a plant-based butter alternative and use almond or oat milk in place of regular milk.

Can I use an unfed sourdough starter?

Absolutely. This recipe doesn’t use the wild yeast in the starter to rise the batter so discard will work just fine.

Can I long ferment this recipe?

Yes! Mix the flour, melted butter, water, and sourdough starter together. Cover, and allow the dough to ferment 12-24 hours at room temperature. The next day, preheat the oven and then mix the remaining ingredients in.

Find More Delicious Fresh Milled Recipes:

If you try this recipe and love it, I would love if you could come back, comment on the post, and give it 5 stars! Please and thank you. Tag me @ablossominglife

Cook Mode

Preheat your oven to 375°F (190°C). Line a muffin tin with muffin liners or lightly grease it to prevent sticking.
In a large mixing bowl or the bowl of stand mixer, whisk together the sourdough starter, eggs, sugar, melted butter, and vanilla extract.
In another bowl, whisk together the freshly milled white wheat flour, salt, baking powder, and baking soda.
Gradually add the dry mixture into the wet ingredients, stirring gently as you go. If it’s too thick, add a tablespoon of milk at a time to adjust the consistency
Once your batter is mixed, fold in the chocolate chips. Be careful not to overmix, as this could result in dense muffins.
Spoon the batter into the muffin tin, filling each cup about 2/3 full. This ensures the muffins have room to rise without overflowing. I like to use an ice cream scoop.
Place the muffin tin in the oven and bake for 18–22 minutes or until a toothpick inserted into the center comes out clean. The tops should be lightly golden brown.

If you’re new to freshly milled flour, note that it can be a bit more absorbent than store-bought flour. If your batter seems too thick, add a little more milk, a teaspoon at a time, until you reach the desired consistency.
These muffins can be stored at room temperature in an airtight container for 2–3 days, or you can freeze them for up to 3 months. To freeze, place them in a freezer bag and store for up 3 months or more.