Last Updated on September 11, 2026 by Kimberly
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It is officially pumpkin season! I love baking pumpkin-flavored everything. One of my family’s favorite pumpkin recipe is these pumpkin chocolate chip muffins with fresh milled flour. The pumpkin flavor combined with chocolate is unexpected, but so delicious!
Why You’ll Love Pumpkin Chocolate Chip Muffins with Fresh Milled Flour
Simple and Easy Recipe – This pumpkin chocolate chip muffin recipe is very easy to make.
Flavor – The flavor of pumpkin with the chocolate chips pairs so well!
Nutrition – Fresh milled soft white wheat flour is full of fiber, vitamins, minerals, and antioxidants.
Ingredients & Substitutions for Pumpkin Chocolate Chip Muffins with Fresh Milled Flour
- Butter
- Organic sugar – I prioritize organic sugar because it helps us avoid glyphosate.
- Eggs
- Vanilla
- Pumpkin Puree – The main ingredient! I love pumpkin-flavored everything.
- Water
- Fresh milled soft white wheat flour – Fresh milled soft white wheat flour is my flour of choice for non-yeast recipes. You can substitute all-purpose flour if you do not have fresh milled flour.
- Baking soda – I buy baking soda in bulk from Costco.
- Baking powder – Aluminum-free baking powder is easy to find online.
- Salt – I use sea salt in my baking recipes.
- Pumpkin Pie Spice – Pumpkin pie spice is essential for fall baking!
- Chocolate Chips
How to Make Pumpkin Chocolate Chip Muffins with Fresh Milled Flour
1: To begin, preheat oven to 375°F.
2: Mill soft white wheat berries in an electric mill.
3: Melt one stick of butter on the stovetop or microwave. Allow to cool slightly.
4: If desired, place a stainless steel mixing bowl on a kitchen scale and weigh your ingredients instead of using measuring cups. I place both weight and measuring cup amounts for the ingredients in the recipe card. Put melted butter and sugar in this bowl and cream.
5: Add eggs, vanilla, pumpkin puree, and water and mix again.
6: In a separate bowl, combine soft white fresh milled flour, baking soda, baking powder, salt, and pumpkin pie spice and stir.
7: Add dry ingredients slowly to wet ingredients, mix well. Fold in chocolate chips.
8: Line a muffin pan with cupcake liners or grease thoroughly. Put three tablespoons of batter in each liner. Let batter rest for ten minutes.
9: Bake at 375°F for 5 minutes, then reduce the oven to 350°F for 20 minutes or until done.
10: Cool in the muffin pan for five minutes, then transfer muffins to a cooling rack.
Pumpkin Chocolate Chip Muffins with Fresh Milled Flour
Ingredients
- 1/2 cup butter, melted
- 1 cup granulated sugar 227g
- 2 eggs, room temperature
- 1 tsp vanilla
- 3/4 cup plus 1 tbsp pumpkin puree 222.4g
- 1/3 cup water 67.5g
- 2 cups plus 8 tbsp fresh milled soft white wheat flour 264.2g Can substitute all-purpose flour. Use 1 2/3 cups of flour for this option.
- 1 tsp baking soda 3.4g
- 1/2 tsp baking powder 0.9g
- 1 tsp sea salt 5g
- 1 tsp pumpkin pie spice 2.5g
- 1 cup chocolate chips 161.1g
Instructions
- Preheat oven to 375°F. Line a 12-cup muffin pan with liners.
- Melt the butter and let it cool until warm but not hot.
- Mill soft white wheat berries in an electric mill.
- If using a scale, weigh out the sugar, vanilla, water, and pumpkin puree required for this recipe. Simply use measuring cups if not using a kitchen scale. Put melted butter and sugar in a mixing bowl and cream.
- Add vanilla, water, and pumpkin puree and mix.
- If using a scale, weigh out the flour, baking soda, baking powder, salt, and pumpkin pie spice required in the recipe. Simply use measuring cups if not using a kitchen scale. Add all ingredients to a stainless steel mixing bowl and stir to combine.
- Add dry ingredients to the wet ingredients. Mix well.
- Gently fold in 1 cup of chocolate chips. Let batter rest for ten minutes.
- Line a muffin pan with cupcake liners. Fill each liner with 3 tablespoons of muffin batter.
- Bake at 375°F for 5 minutes. Reduce the oven temperature to 350°F and bake for an additional 20 minutes or until done.
- Cool in the muffin pan for 5 minutes, then transfer muffins to a baking rack to finish cooling.
How to Store and Reheat Pumpkin Chocolate Chip Muffins with Fresh Milled Flour
Airtight Container – Allow muffins to completely cool. Place in an airtight container with lid or in a plastic storage bag. You can store on the counter for 2-3 days. I do not recommend putting muffins in the refrigerator. They will become dry.
Freezer – To freeze, place in a freezer-safe container with lid or in a freezer bag. For best flavor, use within two to three months.
Reheating – Set muffins on kitchen counter overnight to thaw.
FAQS
I don’t have fresh milled flour. Can I still make pumpkin chocolate chip muffins?
Yes, you can substitute 1 2/3 cup of all-purpose flour.
Can I make pumpkin chocolate chip muffins ahead of time?
Yes! If making more than a day in advance, I would advise sticking the muffins in the freezer to retain freshness.
More Fresh Milled Flour Muffin Recipes!
Banana Bread Muffins with Chocolate Chips – A family classic! This recipes calls for soft white wheat flour and plenty of chocolate chips.
Einkorn Flour Blueberry Muffins – A must for blueberry lovers! This recipe also uses fresh milled einkorn flour.
Einkorn Flour Sour Cream Chocolate Chip Muffins – These muffins are so tasty! I make this recipe when I have sour cream I need to use up in the fridge.
The Best Classic Einkorn Banana Muffins – A classic banana muffin recipe made with a secret ingredient, fresh-milled einkorn flour. This ancient grain gives theses muffins a rich, nutty flavor and wholesome nutrition that sets them apart from ordinary banana muffins.
Fresh Milled Flour Chocolate Zucchini Muffins – These chocolate zucchini muffins are rich, moist, and made with fresh milled flour for extra nutrition. Shredded zucchini keeps them tender while cocoa powder gives them a deep chocolate flavor, a delicious way to sneak in some veggies without sacrificing taste.
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