These zucchini muffins with chocolate chips and almond butter are the coziest fall treat. They’re warm from the cinnamon, sweet from the maple syrup, and decadent from the almond butter center– all while being healthy from the 100% whole wheat.

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Table of Contents
I love having a garden. I have ever since I was a little girl. But maybe the most bittersweet part of having a garden is the day every season where everything has to be pulled up. Green tomatoes come off the vine, herbs end up in a pile to be stored, the last of the potatoes are pulled, and you end up with a pile of half-baked vegetables. And then, the real work begins, and you have to come up with a plan for preserving your hard work. That is the origin story of these muffins.
In years where zucchini are plentiful (that was NOT this year, by the way), I will use a box grater or a grater attachment for the KitchenAid to shred pounds and pounds of zucchini and put them into freezer bags for later use. These get put into the freezer until it’s time to use them.
Muffins are my FAVORITE way to use zucchini up. It’s an easy way to sneak something green into our breakfast, and the zucchini makes these muffins so moist! They’re also foolproof! When I say I have made these every-which-way, I mean it. I’ve used different kinds of flour, skipped the nut butter, subbed out carrots for zucchini, forgotten the baking powder, and they still always turn out delicious (minus the last one– that was not my favorite batch!).
Ingredients
- 2-3 Medium Zucchinis– I added 3/4 cup of shredded zucchini with the water squeezed out
- 1 1/2 Sticks Melted Butter– I like to melt mine in a cast iron skillet, as a healthier alternative to the microwave.
- ½ Cup Maple Syrup
- 3 Large Eggs
- 2 Teaspoons Vanilla Extract
- 2 Cups Whole Wheat Flour– For this recipe, I milled 1 1/2 cups hard white wheat flour.
- 1 ½ Teaspoon Baking Soda
- ½ Teaspoon Salt– I use Redmond’s Real Salt from Azure Standard
- 1 Teaspoon Cinnamon
- ¾ Cup Semi-sweet Chocolate Chips
- 1/3 Cup Almond Butter

Tools You May Need
Glass Bowl– I love that these have lids.
Wooden Spoon
Stainless Steel Measuring Cups
Cookie scoop
Grain Mill– If you are milling your own flour, use this link for $20 off your purchase!
Box Grater
How To Make Zucchini Muffins With Chocolate Chips and Almond Butter
The first step is to get as much water out of the zucchini as you can.
- If you are using fresh – Shred the zucchini and place into a tea towel. Lightly salt the zucchini, and let it sit for a few minutes. After about 5 minutes, squeeze as much water as you can out of the zucchini.
- If you are used frozen shredded zucchini – Let thaw on the counter until the water and the zucchini separate. Drain as much water as you can from the zucchini, then use a tea towel to squeeze the remaining water out of the zucchini.

Preheat the oven to 350 degrees, and prepare a muffin pan with parchment liners. These are my all-time favorite!
If you are using fresh milled flour, mill about 1 1/2 cups of hard white wheat berries!
In a medium-sized bowl, combine the shredded zucchini, melted butter, maple syrup, eggs, and vanilla extract. Mix until these are well combined. Then, into the bowl with the fresh milled flour, add the baking soda, salt, and cinnamon. Mix these together, as well.


Once everything is combined, pour the dry ingredients into the bowl with the wet ingredients and mix well. This is a thicker muffin batter!
Add any desired mix-ins. We go with chocolate chips, but pecans or walnuts would also be lovely.
Now this step is what makes these muffins the BEST! Add a small cookie scoop of muffin batter to the prepared muffin tin. Then use the back of the cookie scoop to flatten. In each muffin tin, add one teaspoon of almond butter. Then, top off with another scoop of muffin batter.

Put the zucchini muffins in the oven at 350 degrees for 20-25 minutes. This batch took about 21 minutes to cook for us!
Serve with a cup of coffee or a big glass of milk while warm. Your family will LOVE these cozy almond butter zucchini muffins as a rich fall treat!
Tips for Making Zucchini Muffins With Chocolate Chips and Almond Butter
- These muffins are a great way to use up the last of the almond butter or peanut butter in the jar! Since we buy almond butter where that is separated, I will make these muffins with the solid almond butter at the bottom of the jar that doesn’t have much oil left in it.
- For an even more beautiful appearance, sprinkle a little extra cinnamon on top of the muffins before you put them in the oven.

FAQs
Can I use a different kind of nut butter or seed butter in these muffins?
Yes! These muffins would be great for
Where can I get fresh milled flour?
If you are in the Middle Tennessee area, you can purchase it from us, here! Fresh milled flour is best used within 3 days of milling for optimal nutrition, so I don’t recommend getting it shipped to you.
I would recommend getting a grain mill, if you don’t have someone near you who sells fresh milled flour. We use ours everyday, and it is my favorite small kitchen appliance. We use a NutriMill grain mill! Use this link for $20 off your purchase!
Are whole grains good for you?
Eating grains whole and intact, the way God designed them, are great for you! That is why, in our home, we strive to use fresh milled whole wheat in every recipe we eat. Flour prepared this way has more fiber and more vitamins and nutrients.
For more information on this, check out this post.
Can I make these zucchini muffins gluten-free?
Yes, you can! Just use 1 cup oat flour and 1 cup brown rice flour.
Storing Zucchini Muffins With Chocolate Chips and Almond Butter
Once baked, you can leave these on the counter for 2-3 days, or freeze for up to 6 months! Just add to a gallon-sized freezer bag and be sure to label it.
Just place in the oven for a few minutes to warm the muffins back up before serving again!
Best Zucchini Muffins With Chocolate Chips and Almond Butter
These zucchini muffins with chocolate chips and almond butter are the coziest fall treat. They're warm from the cinnamon, sweet from the maple syrup, and decadent from the almond butter center– all while being healthy from the 100% whole wheat.
Ingredients
- 2-3 Medium Zucchinis (3/4 cup of shredded zucchini with the water squeezed out)
- 1 1/2 Sticks Melted Butter
- ½ Cup Maple Syrup
- 3 Large Eggs
- 2 Teaspoons Vanilla Extract
- 2 Cups Whole Wheat Flour (1 1/2 cups fresh milled hard white wheat)
- 1 ½ Teaspoon Baking Soda
- ½ Teaspoon Salt
- 1 Teaspoon Cinnamon
- ¾ Cup Semi-sweet Chocolate Chips
- 1/3 Cup Almond Butter
Instructions
Start by shredding the zucchini and getting as much water out as you can. If using fresh zucchini, lightly salt the zucchini, and let it sit for a few minutes. After about 5 minutes, use a tea towel to squeeze as much water as you can out of the zucchini. If using frozen shredded zucchini, let thaw on the counter until the water and the zucchini separate. Drain as much water as you can from the zucchini, then use a tea towel to squeeze the remaining water out of the zucchini.
Preheat the oven to 350 degrees, and prepare a muffin pan with parchment liners.
If you are using fresh milled flour, mill about 1 1/2 cups of hard white wheat berries!
In a medium-sized bowl, combine the shredded zucchini, melted butter, maple syrup, eggs, and vanilla extract. Mix until these are well combined. Then, into the bowl with the fresh milled flour, add the baking soda, salt, and cinnamon. Mix these together, as well.
Once everything is combined, pour the dry ingredients into the bowl with the wet ingredients and mix well. This is a thicker muffin batter!
Add in the chocolate chips and any other desired mix-ins.
This step is what makes these muffins the BEST! Add a small cookie scoop of muffin batter to the prepared muffin tin. Then use the back of the cookie scoop to flatten. In each muffin tin, add one teaspoon of almond butter. Then, top off with another scoop of muffin batter.
Put the zucchini muffins in the oven at 350 degrees for 20-25 minutes. This batch took about 21 minutes to cook for us!
Serve with a cup of coffee or a big glass of milk while warm. Your family will LOVE these cozy almond butter zucchini muffins as a rich fall treat!
Notes
- For gluten-free, I sub 1 cup oat flour and 1 cup brown rice flour.
More Delicious Muffin Recipes
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If you try this recipe and love it, please leave a review! And take a picture and tag me on Instagram @barefootandaproned! I would love to see the muffins you make for your family!




What a great way to use all those garden-fresh zucchini!! This year we didn’t have much luck with zucchini, but I’m saving this for next season. Yum!! Thanks for sharing 🙂
Zucchini wasn’t great for us either this year! We did much better with tomatoes.
I always love finding new ways to use zucchini so will be trying this for sure.