Chocolate Chip Muffins with Fresh Milled Flour
If you love chocolate chips, you need to try these Chocolate Chip Muffins with Fresh Milled Flour! They’re soft, buttery and have plenty of chocolate chips in every bite. They’re easy to make and perfect for breakfast or a snack.
Are you looking for more Freshly Milled Flour Recipes? Try our Einkorn Chocolate Banana Muffins, Pumpkin Muffins, or Cinnamon Sugar Donut Muffins.

SAVE THIS RECIPE FOR LATER!
Just look at all that chocolate! I wasn’t going for a muffin with a few chocolate chips scattered throughout. I wanted chocolate from top to bottom, so these get a full 255 grams of chocolate chips!
These chocolate muffins are so easy to make. No mixer needed and no creaming butter! Mix the batter, give the fresh milled flour a short rest to hydrate, and add the chocolate chips and they’re ready for the oven!
What you’ll love about these Chocolate Chip Muffins
Recipe Ingredients:
You’ll need the following ingredients to make these Fresh Milled Flour Chocolate Chip Muffins:
- Fresh Milled Flour
- Baking powder
- Baking soda
- Salt
- Granulated sugar
- Light brown sugar
- Eggs
- Buter
- Buttermilk
- Sour cream
- Vanilla extract
- Semisweet chocolate chips

Ingredient Notes:
- Fresh Milled Flour: I use soft white wheat for these muffins because it gives them a softer, more tender texture than hard wheat.
- Buttermilk: Use real, full-fat buttermilk. It helps keep the muffins soft and works with the baking soda in the batter.
- Sour cream: Use full-fat sour cream for the best texture.
- Butter: Let the melted butter cool slightly before mixing it with the other wet ingredients.
- Chocolate Chips: Use your favorite brand because you can really taste the chocolate in these muffins! Sprinkle the reserved chocolate chips lightly over the tops rather than pushing them down into the batter.
How to make Chocolate Chip Muffins with Fresh Milled Flour
Grab the full recipe card with exact ingredient amounts below
Step 1: Preheat the oven to 375°F and line a 12-cup muffin pan with paper liners.
Step 2: Whisk the freshly milled soft white wheat flour, baking powder, baking soda, and salt together in a medium bowl.
Step 3: In a large bowl, whisk together the granulated sugar, brown sugar, and eggs. Add the melted butter, buttermilk, sour cream, and vanilla and whisk until combined.
Step 4: Add the dry ingredients to the wet ingredients. Gently fold just until no dry flour remains. Do not overmix.
Step 5: Let the batter rest for 10 minutes to allow the freshly milled flour to hydrate.
Step 6: Fold most of the chocolate chips into the batter, saving about 1/4 cup for the tops.
Step 7: Divide the batter evenly between the 12 muffin liners and sprinkle the remaining chocolate chips over the tops without pressing them into the batter.
Step 8: Bake for 18-22 minutes, or until the tops are set and a toothpick inserted into the muffin portion comes out clean or with a few moist crumbs.
Step 9: Cool the muffins in the pan for 5 minutes, then transfer them to a cooling rack.
NOTE: The flour measurement is for the flour after the wheat berries have been milled. I never use flour while it is still warm from the mill. Place it in the freezer to cool before adding it to the dough.

PRO TIP:
Use full-fat cultured buttermilk for this recipe.Low-fat buttermilk can be thinner and I do NOT recommend homemade buttermilk made wit milk and vinegar or lemon juice. A thinner buttermilk can make the batter too loose and may cause the muffins to sink as they cool. The batter should be thick, not thin and pourable.

Storage and Reheating:
Storage: Store leftover muffins in an airtight container at room temperature for up to 2-3 days.
Reheating: Microwave a muffin for about 10-15 seconds. This is just enough to warm it slightly and soften those chocolate chips again.
Freezing: Let the muffins cool completely, then place them in a freezer-safe container or bag. Thaw at room temperature or warm briefly in the microwave before serving.

Additions and Substitutions:
Chocolate Chips: Semisweet chocolate chips are my favorite for these, but milk chocolate or dark chocolate can be used instead.
Flour: I developed this recipe with freshly milled soft white wheat. Einkorn should also work, but the final texture may change.
Chocolate: Try mixing two kinds of chocolate chips together, or add a few chocolate chunks to the tops.
FAQs about Chocolate Chip Muffins with Fresh Milled Flour
Why are my chocolate chip muffins dense?
The batter may have been mixed too much after adding the flour. Gently fold the wet and dry ingredients together and stop as soon as you don’t see any dry flour.
How do I know when chocolate chip muffins are done?
The tops should be set and a toothpick inserted into the muffin should come out clean or with a few moist crumbs. Be careful not to stick the toothpick through a melted chocolate chip or it may look like the muffin isn’t finished baking.
Why did my chocolate chip muffins sink in the middle?
If your muffins sink after baking, the batter may have been too thin. I recommend using full-fat buttermilk for this recipe. A thinner buttermilk, including some low-fat varieties, can add more moisture and change the consistency of the batter. Over mixing, underbaking, or opening too early can also cause muffins to sink.
Watch the batter: It should be thick enough that it doesn’t pour like a thin cake batter!
Can I use hard white wheat?
Soft white wheat is my favorite for this recipe becasue it gives the muffins a softer texture. Hard white has more protein and will give you a different texture.
What can I serve with chocolate chip muffins?
Honestly, these don’t need much of anything! They’re one of those muffins my kids will grab straight off the counter for a light breakfast, but more often for a sweet snack. They’re especially good when they’re still a little warm and the chocolate chips are soft!
Ready to Bake More with Fresh Milled Flour
If you’re ready to do more with freshly milled flour, check out my Complete Guide To Freshly Milled Flour. It has everything I wish I had when I first started milling my own flour!
You can also grab my Lunchbox Dough eBook, where One Fresh Milled Master Dough can be turned into 10 different handheld meals that are perfect for lunches, quick dinners, and meal prep!
Made this recipe? I’d love to see it! Tag me on IG or FB @littlechefwithin or share a photo in my Facebook group Fresh Milled Flour Happiness. I love seeing what you’re baking!

Chocolate Chip Muffins with Fresh Milled Flour
Equipment
Ingredients
- 250 g freshly milled soft white wheat flour 2 cups
- 7 g baking powder 2 teaspoons
- 3 g baking soda 1/2 teaspoon
- 3 g salt 1/2 teaspoon
- 140 g granulated sugar 2/3 cup
- 25 g light brown sugar 2 Tbsp, packed
- 2 large eggs
- 6 tablespoons butter melted
- 1/2 cup full-fat buttermilk
- 85 g sour cream 1/3 cup
- 8 g vanilla extract 2 teaspoons
- 255 g semisweet chocolate chips 1 1/2 cups, divided
Instructions
- Preheat oven to 375°F. Line a 12-cup muffin pan with liners.
- Whisk together the freshly milled soft white wheat flour, baking powder, baking soda, and salt.250 g freshly milled soft white wheat flour,7 g baking powder,3 g baking soda,3 g salt.
- In a large bowl, whisk together the granulated sugar, brown sugar, eggs, melted butter, buttermilk, sour cream, and vanilla.140 g granulated sugar,25 g light brown sugar,2 large eggs,6 tablespoons butter,1/2 cup full-fat buttermilk,85 g sour cream,8 g vanilla extract.
- Add the dry ingredients to the wet ingredients and stir just until combined.
- Let the batter rest for 10 minutes to allow the freshly milled flour to hydrate.
- Fold 181 g (1 1/4 cups) of the chocolate chips into the batter.255 g semisweet chocolate chips.
- Divide the batter evenly among the muffin cups. Sprinkle the remaining 43 g (1/4 cup) chocolate chips evenly over the tops.
- Bake for 18 to 22 minutes, or until the tops are set and a toothpick inserted into the muffin portion comes out with a few moist crumbs.
- Cool in the pan for 5 minutes, then transfer to a wire rack.
Notes
Nutrition
This post contains links to affiliate websites, such as Amazon, and we receive an affiliate commission for any purchases made by you using these links. We appreciate your support!
About Vicky Hadley
Vicky Hadley is a professional food photographer and creator behind Little Chef Within. As a mom of 6 boys, there’s always plenty of noise and plenty of food! She relies on filling meals to keep her crew happy and loves creating recipes that real families can count on.


