Last Updated on July 16, 2026 by Kimberly
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Last year we planted zucchini in our garden and had a bumper crop. We had so much zucchini! I finally started dicing it in the food processor and storing in the freezer for later. These fresh milled flour chocolate zucchini muffins are a great way to use up either fresh or frozen zucchini!
Why You’ll Love Chocolate Zucchini Muffins
Simple and Easy Recipe – These chocolate zucchini muffins are so easy to quickly mix up. They make a great breakfast paired with scrambled eggs, a good snack, or even dessert!
Flavor – Soft white wheat gives these chocolate muffins more depth of flavor than regular flour.
Nutrition – Fresh milled soft white wheat flour is full of fiber, vitamins, minerals, and antioxidants.
Ingredients & Substitutions for Fresh Milled Flour Chocolate Zucchini Muffins
- Fresh milled soft white wheat flour – I love using fresh milled soft white wheat flour in muffins.
- Cocoa powder – Zucchini and chocolate go so well together.
- Baking soda – I buy baking soda in bulk from Costco.
- Salt – Helps balance out the sugar in this recipe.
- Baking powder – Helps the muffins rise,
- Olive oil – The fat needed for this recipe.
- Organic sugar – I buy organic sugar to avoid glyphosate.
- Eggs – Hold the batter together. You can substitute Bob’s Red Mill Egg Replacer if needed.
- Vanilla extract – Vanilla adds so much flavor to baking.
- Zucchini -The star of the show! You can use fresh or frozen zucchini for this recipe.
- Chocolate chips – Chocolate chips make these muffins extra chocolaty!
How to Make Chocolate Zucchini Muffins
Step 1: Mill soft white wheat berries in an electric mill.
Step 2: If desired, place stainless steel mixing bowl on a kitchen scale and weigh your ingredients instead of using measuring cups. I place both weight and measuring cups amounts for the ingredients in the recipe card. Add the fresh milled flour, cocoa powder, baking soda, salt, and baking powder to this bowl.
Step 3: In a separate bowl on your stand mixer, measure out olive oil and sugar (by weight or using measuring cups) and mix together. Add eggs and vanilla extract and mix thoroughly.
Step 4: Slowly add dry ingredients to wet ingredients, a little at a time. Mix until just combined.
Step 5: Fold in zucchini, then chocolate chips with a silicone spatula.
Step 6: Line a muffin tin with cupcake liners. Fill each liner with 3 tablespoons of batter.
Step 7: Bake at 350°F for 20 minutes or until done.
Chocolate Zucchini Muffins with Fresh Milled Flour
Ingredients
- 3 3/4 cups fresh milled soft white wheat flour 453.5g Can substitute 3 cups all-purpose flour.
- 1/3 cup cocoa powder 31.9g
- 1 tsp baking soda 6g
- 1 tsp salt 6g
- 1/4 tsp baking powder 0.4g
- 1 cup olive oil 224g
- 2 cups organic sugar 469.6g
- 3 eggs 155.4g Can substitute Bob's Red Mill Egg Replacer.
- 3/4 cup previously frozen, thawed, diced zucchini, water removed 166.2g Can substitute 2 cups fresh diced zucchini. Be sure to wring the water out!
- 1 1/2 cups chocolate chips 241.1g
Instructions
- Mill soft white wheat berries in an electric mill.
- If using a scale, place mixing bowl on kitchen scale and add flour, cocoa powder, baking soda, salt, and baking powder by weight. If using measuring cups, measure out dry ingredients.
- In a separate bowl on your stand mixer, measure out olive oil and sugar (by weight or using measuring cups). Using a stand mixer, beat these two ingredients until incorporated. Then add the eggs and vanilla.
- Slowly add the dry ingredients to the wet ingredients until just combined. Do not overmix.
- Fold in zucchini and chocolate chips with a spatula.
- Place cupcake liners in a muffin tin. Fill with 3 tablespoons of batter.
- Bake at 350°F for 20 minutes or until an instant read thermometer reads 200°F-205°F.
- Let cool on wire baking rack.
- If you make this recipe, please scroll to the comments and give it a rating. This helps my website so much!
How to Store and Reheat Chocolate Zucchini Muffins
Airtight Container – Allow chocolate zucchini muffins to cool completely on a wire baking rack. Store in an airtight container or storage bag for three to five days.
Freezer Bags – If making ahead of time, store chocolate zucchini muffins in the freezer. Thaw overnight on the kitchen counter for an easy make-ahead breakfast.
FAQS
I don’t have fresh milled flour. Can I still make these chocolate zucchini muffins?
Of course! You can substitute all-purpose flour. Simply use 3 cups of flour for this option.
Can I make these chocolate zucchini muffins ahead of time?
Of course you can! If making more than a day in advance, I would advise sticking them in the freezer to retain freshness.
One of my family members has an egg allergy, can I substitute the egg for something else?
Yes! My husband has an egg white allergy, so I use Bob’s Red Mill Egg Replacer often in my baking. The muffins will be a little crumbly if you substitute.
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.
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