This chocolate zucchini muffin recipes uses fresh milled flour and sourdough discard to make delicious, moist, chocolatey treats that you won’t believe are nourishing for you. You will want to eat these on repeat! This is a perfect recipe during the summer months when you are up to your ears in garden zucchini.

Top view of chocolate sourdough discard muffins with zucchini and fresh milled flour.

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One of my favorite past times is taking yummy recipes and transforming them into healthier versions. Zucchini bread / muffins are already on their way to being a healthier version to an original, but I wanted to also add in sourdough discard, fresh milled grains, and cut out the refined sugar for a snack that I know is great for my kids (and me!). The result? Oh so moist, gooey, chocolatey muffins that I can’t stop eating.

Reasons To Love This Recipe

Use Up Your Extra Sourdough Discard – I don’t know about you, but I hate when I have to throw away sourdough starter. These muffins are the perfect way to use that extra discard sitting in your fridge.
Naturally Sweetened – This recipe uses maple syrup (or honey) instead of refined sugar, and the muffins are still perfectly sweet.
Eat More Veggies! – Thanks to shredded zucchini, these muffins are really moist and are a great way to sneak some veggies to your kids. They probably won’t even notice it’s in there.
Better Nutrition from Fresh Milled Flour – 100% whole wheat flour made from fresh milled whole grains means better flavor, texture, and all the nutrients found in the original grain. These chocolate muffins truly are a healthy snack that you can make on repeat.
Chocolate + Zucchini = A Match Made In Heaven – Rich chocolate flavor masks the zucchini completely but stays really moist. I often wonder who was the first person to add zucchini to bread? I’m not sure, but I owe them a thank you card. The zucchini is definitely key to the great texture.
Great for Breakfast, Snack, or Dessert – Enjoy them warm out of the oven, pack them in lunchboxes, or enjoy with a cup of coffee as a mid-morning pick me up. No wrong way to eat these chocolate muffins!
Freezer-Friendly – Make a double batch and freeze extras for quick, grab-and-go snacks anytime. Set them out at room temperature to thaw them or heat in the microwave.

Several dark chocolate muffins cooling on a wire rack.

Why Fresh Milled Flour?

I’ve been really into fresh milled flour over the past year, and my obsession is growing the more I learn! There’s so many fascinating health benefits to milling flour fresh as you bake with it. The primary reason for me, is that the wheat berry starts to lose nutrients as soon as it is exposed to oxygen. That means as soon as it is milled into flour, valuable nutrients (20 essential nutrients!) begin to depreciate. After just 24 hours, 40-45% of the nutrients are gone, and after three days, 90%! I have been trying to completely make the switch to fresh milled flour, and I’m learning that all of my favorite treats are just as good, if not better.

If you want more fresh milled flour recipes, some of my favorite are fresh milled flour pancakes, fresh milled cream of wheat, and fresh milled sourdough bread.

Ingredients in Chocolate Zucchini Muffins With Fresh Milled Flour

This recipe uses nothing but nourishing ingredients to create such a wholesome treat. Here’s what you will need:

Sourdough Discard – Adds a touch of flavor and adds to the texture of these muffins.

Coconut Oil – a great alternative to vegetable oil, coconut oil is my go-to when baking. It has so many health benefits and doesn’t make your baked goods taste like coconut.

Real Maple Syrup – my favorite natural sweetener to use in place of sugar. Make sure you use real, pure maple syrup, and not the fake stuff.

Egg – pastured eggs are the best!

Milk – I use raw, whole milk in this recipe. You can use whatever you drink.

Vanilla, Salt, Baking Powder & Baking Soda

Fresh Milled Flour – I use soft white wheat and it works great.

Organic Cacao Powder – Real, organic cacao give these muffins the best decadent flavor. It’s so perfectly rich.

Grated Zucchini – finely grated works best so that it can mix evenly into the muffin batter.

Dark Chocolate Chips – Not absolutely necessary, but a high quality dark chocolate chip really adds to the taste of these muffins. I get dark chocolate chips in bulk from Azure Standard and they are really the best.

Other Supplies You Will Need

Grain Mill – the secret to milling your own flour. It is near to impossible to find freshly milled flour for sale, so milling your own is the best way to enjoy all of the benefits. I have been using the MockMill 100 and it’s worked really well.
Two mixing bowls
Cheese or Vegetable Grater – I like my box grater that has a super fine side
Muffin Tin & Liners

Close up view of three chocolate zucchini muffins with a bite taken out.

How To Make Sourdough Discard Chocolate Zucchini Muffins With Fresh Milled Flour

With a few easy steps, these chocolate muffins will be ready in no time!

Step 1: Preheat the oven to 350, and line a muffin tin with paper liners. Alternatively, you can grease your muffin tin with butter or coconut oil.

Step 2: Grind the wheat berries using the fine setting on your grain mill.

Step 3: In a large mixing bowl, combine flour, cacao powder, baking powder, baking soda, and salt. Mix everything together.

Step 4: In a separate small mixing bowl, combine sourdough discard, melted coconut oil, and maple syrup. Whisk to combine.

Step 5: To the wet ingredients add the egg, milk, and vanilla extract. Whisk again until mixed together really well.

Step 6: Prep the zucchini. Wash it, chop off the ends, and use a box grater to shred the zucchini on the finest side. Don’t overdo it, but you can squeeze a little bit of the excess moisture out of the zucchini if it’s extra juicy.

Step 7: Combine the wet ingredients with the dry ingredients. Gently stir until partially combined, and then add the zucchini shreds and chocolate chips. Mix everything together until just combined, try not to over-mix the muffin batter.

Top view of a bowl with chocolate zucchini muffin ingredients

Step 8: Scoop the batter into the prepared muffin pan. Fill each one about 3/4 full or about 1/3 cup of batter. This recipe makes about 12 muffins.

Step 9: Bake muffins for 15-17 minutes or until a toothpick inserted into the center comes out mostly clean (some chocolate from the chocolate chips is ok).

Close up view of chocolate zucchini muffins with fresh milled flour on a white plate

Step 10: Let the muffins cool for a few minutes before transferring them to a wire rack to cool. Enjoy your healthy chocolate treat!

Tips For Perfect Muffins

This recipe is pretty fool-proof, but here are some tips to make your muffins turn out perfect every time:

Try not to over-mix the batter
If your zucchini is really juicy / watery, squeeze the excess liquid out before mixing it into the batter.
Don’t overfill the muffin tins. 3/4 full is perfect.

Variations And Add-Ins

Use this recipe as a base, and experiment with some variations. You could try:

Adding chopped walnuts or pecans
Swap zucchini for shredded carrots
Use honey instead of maple syrup

Serving Suggestions for Chocolate Zucchini Muffins With Fresh Milled Flour

I think you will find yourself grabbing these muffins and enjoying them plain anytime you walk through the kitchen, but here are some other ideas:

Warm with almond butter or peanut butter.
Crumbled into Greek yogurt with fruit.
Warm with a scoop of vanilla ice cream
Packed into lunchboxes for kids
Quick grab-and-go breakfast or snack

Close up view of four chocolate muffins with chocolate chips on a cooling rack

How To Store Extra Chocolate Zucchini Muffins

These muffins will keep fresh for a few days in an airtight container at room temperature. They freeze really well for longer storage! To freeze, cool completely and put in a freezer-safe or airtight container and store in the freezer for a few months. Thaw them out at room temperature, or speed things up in an oven or microwave.

Frequently Asked Questions

No, not at all! The rich chocolate flavor masks any zucchini flavor.

You could certainly try a gluten-free flour substitute, although I haven’t tried this personally. Something interesting to consider is that many people with gluten intolerances are able to eat fresh milled flour!

Of course! You will end up with a slightly different flavor, but still delicious.

Yes, you can! If you are leaving out the discard, you may need to add a little more milk if the batter is too thick.