Pumpkin Chocolate Chip Muffin Made with Freshly Milled Flour

If you haven’t had a pumpkin chocolate chip muffin recently, you’re missing out! Start with this recipe that is a 10/10 for both flavor and nutrition.

Pumpkin and chocolate are one of the best combinations out there. That’s why these muffins, with their perfect pumpkin flavor and gooey chocolate chips, get made on repeat at the Lavender Blue Cottage. They are scrumptious, healthy and easy to whip up.

I promise that you’ll love this recipe. Partly for the nutritious fresh milled flour it uses, and partly for the out of this world flavor. It’s the perfect treat for a lovely Fall day!

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Special Announcement: My 100% Whole Wheat Yeast Breads with Freshly Milled Flour cookbook is now available! It contains my best-of-the-best yeast bread recipes and lots of great information about milling flour and baking with whole grains. Get your copy today or check out all of my Keeper of the Home cookbooks.

Fresh Milled Flour Makes the Best Muffins

If you know me, you’ll know I love freshly milled flours. I mill all of my flour from wheat berries. It’s a quick and easy process that you can read about in how to mill your own flour and the health benefits.

Fresh milled flour is the best kept secret in baking. In a nutshell, you get the best flavor and the most nutrients from your flours within the first hours and days after they are milled. Quality declines significantly after that.

You have no way of knowing how long a bag of flour has been sitting on your grocery store shelf. That’s why I use fresh milled flour for muffins and everything else. It’s top quality every time!

For tips on how to get perfect muffins every time, checkout my muffin making tips, the best grains for fresh milled flour muffins and muffin testing results.

Pumpkin Chocolate Chip Muffin Ingredients

Wet Ingredients

• ½ cup plain yogurt
• 2 large eggs
• ½ cup honey
• ½ cup melted and cooled coconut oil or butter (or ¼ cup butter + ¼ cup coconut oil)
• 1 teaspoon pure vanilla extract
• 1 cup pumpkin puree

Dry Ingredients

• 2 cups (260 grams) freshly milled flour
• 1 teaspoon salt
• 1 tablespoon pumpkin pie spice
• 1 teaspoon baking powder
• ¾ teaspoon baking soda

Mix-Ins

• ½ – ¾ cup chocolate chips

How to Make Pumpkin Chocolate Chip Muffins

Preheat your oven to 425°F (220°C). Grease a muffin pan or line with paper liners and set aside.

In a large mixing bowl, whisk together all of the wet ingredients until smooth and well combined.  

Add the freshly milled flour, salt, and pumpkin pie spice to the bowl with the wet ingredients. Gently stir just until incorporated. Cover and set aside to let the flour absorb the liquid for 10 minutes.

After resting, sprinkle in the baking powder and baking soda. Mix gently until everything is evenly combined, being careful not to overmix. Fold the chocolate chips into the batter.

Working quickly, spoon the batter into the prepared muffin tin, filling each cup evenly.

Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 10-12 more minutes, or until the centers feel firm and the muffins are baked through.

Remove from the oven and let cool slightly on a wire rack — or enjoy warm right away.

Storing Pumpkin Chocolate Chip Muffins

Store cooled muffins in an airtight container at room temperature for up to 2 days. For longer storage, wrap in plastic wrap and place the muffins in a freezer bag or freezer container the same day they’re baked. Thaw at room temperature before serving.

Printable Pumpkin Chocolate Chip Muffin Recipe Card

Where to Find Baking Supplies

If you need baking supplies, checkout the Bread Making Supplies page. It’s where I share information and links to all my baking favorites. Only the best products make it onto this page!

More Recipes to Try

I’m already dreaming of the next time I can mix up a batch of these moist pumpkin chocolate chip muffins. They really hit the spot for a healthy breakfast, snacking or dessert. Try them for yourself and see what I mean!

If you love muffin recipes, Fall treats or delicious food in general, take a look at some of the goodies below!

• Fresh Milled Flour Chocolate Muffin Healthy Recipe
• Healthy Pumpkin Pie Filling Recipe – So Good!
• The Best Coconut Oil Pie Crust Recipe
• Healthy Pumpkin Smoothie Bowl | Loaded with Nutrition
• Healthy Whole Wheat Pumpkin Crepes
• Healthy Pumpkin Muffins | Quick to Make and So Delicious!
• Cinnamon Apple Muffins Recipe with Fresh Milled Flour
• Healthy Whole Wheat Zucchini Muffin Recipe
• Chocolate Chip Banana Muffin Recipe with Fresh Milled Flour
• Savory Herb and Cheese Muffin with Fresh Milled Flour