Double Chocolate Zucchini Muffins

These sneakily Healthy Chocolate Zucchini Muffins are made with 100% whole-grain flour, plenty of hidden veggies, and have no refined sugar aside from the delightfully melty chocolate chips. Don’t worry though—these terrifically tender treats still taste like dessert!

As a working mom of two, I’m a huge fan of make-ahead, grab-and-go snacks. You never know when someone is going to wake up late, not be able to find a shoe, or any of the other million things that can throw a wrench in your morning routine. 🥴 That’s why pre-portioned breakfasts like these zucchini chocolate chip muffins are so clutch!

But, unlike bakery-style muffins that are really just cakes in disguise, my approach to muffins is with an RDN’s idea of health in mind. (You can check out my healthy blueberry zucchini muffins and healthy lemon zucchini muffins as added proof. 😉) While these double chocolate zucchini muffins might taste naughty, they’re surprisingly virtuous. 

First, I use 100% whole-wheat pastry flour for a hefty boost of dietary fiber and nutrients. Rather than butter, I use heart-healthy avocado oil. I similarly avoid granulated sugar in favor of less-refined coconut sugar, which has a lower glycemic impact and is less likely to cause a spike in blood sugar. And don’t forget—there’s zucchini in there, too!

Jump to:

• What do they taste like?
• Why You’ll Love This Healthy Muffin Recipe
• Ingredients Needed
• Substitutions
• How To Make Zucchini Chocolate Chip Muffins
• Optional Variations & Dietary Adjustments
• Recipe Tips
• Serving Suggestions
• Storage Directions
• Homemade Zucchini Chocolate Chip Muffins Nutrition
• Pricing Info
• FAQs
• Other Muffin Recipes
• Recipe

What do they taste like?

Despite all the healthy bona fides, these chocolate chocolate chip zucchini muffins eat like dessert. They’re rich and chocolatey thanks to a double whammy of dark cocoa powder and mini chocolate chips, slightly toasty from the whole grain flour, and have a cozy undertone from cinnamon and nutmeg. 

Swapping out the butter in favor of oil makes them extra light and springy, while the shredded squash brings tons of moisture (and almost no flavor, for anyone who might be worried). Seriously—my kindergartener would crush the whole lot of ‘em if given the chance. She has no idea there are any veggies in there at all! 🤫

Why You’ll Love This Healthy Muffin Recipe

• Quick & Easy – Aside from grating the zucchini and measuring out your ingredients, the prep work required to make a batch of these chocolatey muffins is minimal. They’ll be ready for the oven in just 10 minutes!
• One & Done – One batch of my double chocolate zucchini muffins makes a dozen, meaning you’ve got snacks or breakfasts for the whole week! Even better, they freeze like a dream, so you can get as far ahead as you need.
• Budget-Friendly – At just over 50 cents a serving, these yummy snacks are a great option if you’re on a tight budget.

Ingredients Needed

I’d consider most of what you need to make this healthy chocolate zucchini muffins recipe a pantry staple. Here’s what to grab:

• Whole Wheat Pastry Flour – Swapping out your old white flour for whole grain pastry flour is one of the easiest ways to boost the nutrient density of all your favorite baked dessert recipes. 
• Unsweetened Cocoa Powder – If possible, opt for Dutch-processed cocoa powder for the richest chocolate flavor and least amount of bitterness. Otherwise, regular cocoa powder (or black cocoa) works great!
• Baking Soda & Baking Powder – You’ll need both types of leaveners to get these muffins to rise to their loftiest heights! They aren’t interchangeable. 
• Cinnamon, Nutmeg, & Salt – Warming spices and a bit of seasoning are all you need to boost the flavor of these spiced chocolate zucchini cake muffins. 
• Coconut Sugar – This is my second favorite healthy dessert recipe swap. Coconut sugar adds a brown sugar-like sweetness with way less of an impact on your blood sugar. 
• Avocado Oil – Of all the neutral-flavored oils, avocado has the best make-up of fats and is the healthiest option for your heart. 
• Large Eggs – Whenever a recipe calls for more than one egg, note that the size does matter. If you’re swapping in another size, note that each large egg is a scant ¼ cup. 
• Grated Zucchini – Make sure you’re grating your own zucchini here rather than using pre-shredded zucchini from the store—those are far too thick for what we need!
• Mini Chocolate Chips – These are double chocolate zucchini muffins, after all!

Substitutions

Fresh out of something you need? Not to worry. Here are some substitutions to try to avoid another run to the grocery store: 

• Whole Wheat Pastry Flour – You can use a 50/50 split of all-purpose flour and regular whole wheat flour to get some of the whole grain benefits while achieving a perfectly soft and light texture. You can also use all AP, but then there’s no whole grains at all. ☹️
• Unsweetened Cocoa Powder – For an added boost of antioxidants, swap in raw cacao powder instead. 
• Cinnamon & Nutmeg – Feel free to omit the warming spices, or swap in your favorites (e.g. pumpkin pie spice). 
• Coconut Sugar – Brown sugar is more refined and has a greater impact on your blood sugar than coconut sugar, but it’ll taste just as good! You can also use maple sugar instead.
• Avocado Oil – Canola oil is a cheaper alternative and still boasts a pretty heart-healthy fat make-up.
• Large Eggs – I haven’t tried it, but I’d bet this zucchini chocolate chip muffins recipe would work well with some common egg substitutes for baking like 2 flax eggs, ½ cup of mashed banana, or ½ cup of silken tofu.
• Grated Zucchini – In case you didn’t already know, summer squash can be used interchangeably with zucchini. Feel free to swap in yellow summer squash, or any fancy CSA varieties you might have kicking around like patty pan or zephyr squash. 
• Mini Chocolate Chips – I like having little bits of chocolate spread evenly throughout the muffin, but you’re welcome to use regular-sized chocolate chips, chocolate chunks, or chopped bar chocolate if you prefer!

How To Make Zucchini Chocolate Chip Muffins

You’ll love how quickly this recipe comes together: 

Step 1: Whisk together dry ingredients in a medium mixing bowl until well-combined. 

Step 2: Whisk together wet ingredients in a separate large mixing bowl.

Step 3: Add the dry ingredients to the wet ingredients and stir to combine. Don’t overmix! The batter will look and feel very dry. This is normal. 

Step 4: Mix in the shredded zucchini. The batter should feel more like cake batter now.

Step 5: Fold in the chocolate chips. Make sure to reserve some for the top!

Step 6: Divvy batter between lined muffin tin liners. Sprinkle the tops of the zucchini muffins with chocolate chips for a professional look. 

Step 7: Bake for 21-23 minutes, or until a toothpick comes out clean. Cool for 5 minutes in the tin, then move to a wire rack to continue cooling. 

Optional Variations & Dietary Adjustments

• Sugar-Free – Swap in your favorite cup-for-cup brown sugar alternative (e.g. monkfruit) and use sugar-free chocolate chips to make these zucchini chocolate muffins sugar-free and diabetic-friendly.
• Like Carob for Chocolate – If you’re super sensitive to the effects of caffeine, chocolate might not feel within reach. Feel free to swap in carob powder and carob chips for a similar flavor profile with zero added caffeine. 
• Other Mix-Ins – Don’t feel limited to chocolate chips as your mix-ins. You can always add or swap in what you want! (Just don’t exceed a total of ¾ cup dry mix-ins, or you’ll risk the muffins falling apart.) Other good options include toasted nuts or dried fruit.

Recipe Tips

• Use a large spring-loaded cookie scoop to make it easy to evenly divide the raw batter without making a mess.
• Out of muffin liners? Use parchment paper to make your own!
• Doubling the recipe? Make sure to rotate your muffin pans from top to bottom halfway through the baking time for even cooking. 
• Don’t overwork the batter. When you first add the dry ingredients to the wet ingredients, it’s going to feel all wrong—super dry, hard to stir, lots of lumps. Don’t worry! Once you add the zucchini and all of its lovely moisture, the batter will loosen and the lumps will mostly dissipate. Just don’t stir the batter too much, or you risk dense, tough muffins.

Serving Suggestions

With all the chocolatey goodness packed into every bite, these zucchini chocolate chip muffins are perfectly delightful to eat on their own, at room temperature with no accoutrements. That said, there’s more than one way to eat a muffin:

• Post Work-Out Snack – Halve your muffin and slather on some (real) peanut butter for an added boost of muscle-building protein and satiety-inducing fat. If you’re feeling extra decadent, a pad of grass-fed butter is always welcome, too.
• Morning Mayhem – Set yourself up for success by having plenty of meals and snacks prepped for the week. These chocolate zucchini muffins are great, but consider making a batch of your favorite protein overnight oats recipes or another one of these healthy muffin recipes so you don’t get bored. (I mean, it’s tough to get bored with chocolate, but it *can* happen. To some people, at least! 😂)
• Caffeination Break – Pair one of these chocolatey treats with your favorite coffee drinks for a fantastic moment of “me time” in the middle of your day. Watching your macros? Consider blending protein powder in your coffee or making my frosty high-protein coffee shake for balance.

Storage Directions

• Room Temperature – Allow any leftover zucchini chocolate chip muffins to cool completely before transferring to an airtight container—this helps prevent condensation from forming and making your muffins soggy. They should keep well on the counter for up to 5 days.
• Freezing – For longer storage, transfer cooled muffins to a freezer bag. If you have the time, consider wrapping them individually in plastic wrap first to help ward off freezer burn. They should keep well for up to a month. (You can eat them past that time, the texture and flavor will just start to deteriorate a bit.)
• Reheating – If defrosting is necessary, remove any packaging and let sit at room temperature for a few hours. You can use a toaster oven to reheat if you like to eat your muffins warm!

Homemade Zucchini Chocolate Chip Muffins Nutrition

At 315 calories a pop, these tender little snacks are perfect for keeping you satisfied between meal times. They each have an impressive 6 grams of protein (not bad for a muffin!) and 5 grams of nutritional fiber (about ⅕ of the daily recommended amount for us ladies, or just over ⅛ – ⅙ the recommended amount for fellas depending on age). 

You’ll also get 13 grams of fat per muffin, which can help you feel more full. Remember that fat isn’t a 4-letter word—you need it in your diet to effectively absorb nutrients and keep your heart and brain happy. You just have to choose the right fat, like the avocado oil we use here. There’s also 46 grams of carbs (but 5 come from fiber) and approximately 260 milligrams of sodium per muffin.

Aside from just the raw numbers, though, remember all the goodies we’re packing in here! Zucchini is a great source of vitamins C and B6, magnesium, potassium, and antioxidants. Whole wheat pastry flour is packed with dietary fiber, iron, and calcium. Eggs have all 9 amino acids, making them a perfect protein, and are also good sources of choline and antioxidants.

So, even though they taste like naughty treats, these double chocolate zucchini muffins are actually pretty darn healthy! Enjoy every bite, guilt-free.

Total nutritional content per muffin is:

• Calories: 315 calories
• Total Fat: 13 grams
• Protein: 6 grams
• Sodium: 260 mg
• Carbohydrates: 46 grams
• Fiber: 5 grams

*This nutritional information is an estimate and calculated based on the ingredients used to create the recipe. The nutritional value of your ingredients may differ slightly. Furthermore, this food is not intended to prevent, diagnose, cure, or treat any disease.

Pricing Info

This is what I personally paid to make this recipe:

• 2 cups whole wheat pastry flour: $0.53
• ½ cup unsweetened cocoa powder: $0.56
• 1 ½ tsp baking soda: $0.02
• 1 tsp baking powder: $0.05
• ¼ tsp cinnamon: $0.01
• ¼ tsp nutmeg: $0.01
• ¼ tsp salt: $0.01
• 1 ⅓ cup coconut sugar: $1.04
• ½ cup avocado oil: $1.48
• 2 large eggs: $0.90
• 1 tbsp vanilla extract: $0.12
• 1 ½ cups shredded zucchini: $0.75
• ½ cup mini chocolate chips: $0.82

The total comes out to be around $6.30 or $0.53 per muffin!

FAQs

Other Muffin Recipes

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Recipe

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xoxo Megan