While driving down I-5 on a long road trip back from visiting my parents recently, I glanced up at the large green sign posted high above the freeway. “Harbor Blvd,” it read. “½ mile.”
I smiled and peeked to my right as the off-ramp appeared. Although almost entirely obscured by large buildings, Disneyland, California Adventure, and all of their attractions and rides sprawled out across the land. Throughout my childhood, Harbor Boulevard was the exit we always took to get to those theme parks and our hotel.
And that hotel materialized the very next second. The tall concrete structure of Howard Johnson’s (or HoJo’s, as we fondly called it!) was “freeway close” and nearly brushed right up against I-5’s walls. Almost a quarter of the rooms looked out over the cars speeding by.
Yet none of that mattered to me as a little girl — the noise, lack of a view, or anything else. We were going to Disneyland! The park was just steps away! I could barely sit still long enough to eat my breakfast.
I grinned as more memories floated through my mind. Instead of cold cereal and milk that required refrigeration, my mom often brought muffins for our early morning meals instead. That felt like such a special treat, peeling back the paper wrappers and licking the soft crumbs from my fingers, and although hopping on rides and meeting the characters were always the best parts of those vacations…
I still looked forward to those 6 am bakery muffins too.
Not too surprisingly, I ended up craving muffins for the final stretch of my road trip… And within an hour of pulling into my garage back at home, my fingers tugged the wrapper off of one of these warm ultimate healthy zucchini muffins. I smiled as I swallowed my first bite. It tasted just as good as the ones from my childhood — if not even better — and was completely worth the wait!
QUICK OVERVIEW – HEALTHY ZUCCHINI MUFFINS
Difficulty: Fairly easy, including for many beginner bakers.
Taste: Cozy and comforting, with warm spices and sweet flavors filling every bite.
Texture: Really moist and tender, with lots of supremely soft zucchini woven throughout the muffin batter.
KEY INGREDIENTS TO MAKE HEALTHY ZUCCHINI MUFFINS
Let’s cover the ingredients you’ll need to make these zucchini muffins! I’m assuming that you already have baking staples like vanilla and salt, so we’ll mainly cover the more interesting and important ones. First up, you’ll need…
Flour. To make these zucchini muffins healthier, I opted for white whole wheat flour. I know, I know… That sounds a little strange — and maybe even like an oxymoron! Yet such an ingredient does actually exist, and it’s not just a combination of whole wheat and white (aka all-purpose!) flours.
Here in the US, farmer grow two main types of wheat: red and white. Red wheat is heartier, and it’s used to make regular whole wheat flour. White whole wheat flour is made by finely grinding (you guessed it!) the other variety, white wheat. White wheat has a lighter appearance, milder flavor, and softer texture. Therefore, white whole wheat flour behaves more like all-purpose flour compared to regular whole wheat flour — but it still has the same health benefits as regular whole wheat flour, like extra fiber and micronutrients.
Basically… It’s the best of all worlds! That’s why white whole wheat flour is one of my all-time favorite flours. I keep it in my pantry at all times!
Hint: It’s similar to the difference between red and green grapes. Different appearance and flavor but similar health benefits!
Tip: If you’d like to make your healthy zucchini muffins gluten free, then see the Notes section of the recipe. I’ve shared my top gluten free recommendations there!
Spices. You’ll need three: cinnamon, allspice, and nutmeg. I love the richness and depth the latter two added to these muffins’ flavor. They made these muffins taste extra cozy, so I promise it’s worth using all three!
Tip: I’m obsessed with Saigon cinnamon! It has a stronger, sweeter, and richer flavor compared to regular cinnamon. It’s really affordable, and I buy it online here!
Egg whites. The protein in the egg whites contributes to the structure of these zucchini muffins and helps prevent them from collapsing while cooling. So yes — you do need to use all of them! However, I understand some people prefer baking with whole eggs. If that’s you, then see the Notes section of the recipe! I’ve included a tip about how to do so there.
Greek yogurt. This is another one of my favorite healthy baking ingredients! In these zucchini muffins, Greek yogurt adds the same moisture to the batter as extra butter or oil but for a fraction of the calories. It also gives your muffins a protein boost!
Tip: Not all Greek yogurts are created equal! For the best results, look for ones that only include milk and live and/or active cultures. (It’s fine if the carton lists the cultures by name in the ingredients!) These Greek yogurts are generally thicker, which will yield a better batter consistency and muffin texture.
My favorite is FAGE plain nonfat Greek yogurt. It has the thickest consistency of any brand that I’ve tried so far, and it also has less of a yogurt “tang” to its flavor. (It makes fantastic frosting too!)
Sweetener. I used liquid stevia to sweeten these healthy zucchini muffins, which means they’re sugar free! Stevia is a plant-based, no-calorie sweetener that contains nothing refined or artificial (aka it’s clean eating friendly!). It’s also highly concentrated. You only need 2 ½ teaspoons to sweeten all 12 muffins!
Many stevia brands and products have different sweetness levels, so they’re not always 1-for-1 substitutes for each other. For the best results, I highly recommend using the same one that I did! I buy it online here because that’s the lowest price I’ve found, and I love how I don’t notice any prominent aftertaste like with some other stevia products. (You’ll also use the same liquid stevia in all of these recipes of mine. I promise it’s not a “one-time use” ingredient!)
Zucchini. Here’s where things got a little nerdy and interesting! If you’ve made any of my other zucchini recipes or carrot recipes before, then you probably know that I love cramming my baked treats full of these two vegetables. That’s especially true for my two-layer carrot cake and carrot sheet cake… They’re almost equal parts batter and carrots!
When I tried that approach to make these muffins, it failed miserably. The muffins collapsed while cooling, and it looked as if someone had tied an invisible belt around their sides and tightened it as far as it could go. It was almost the literal definition of “muffin tops” — truly! The insides of those muffins were also really wet, and although they were definitely baked all the way through, there was an almost raw-like quality to them as well.
And yes… That was even after I had dried the zucchini before adding it to the batter. (More on that in a minute!)
So I went back to the drawing board. I changed the amount of liquid ingredients in one batch, the amount of zucchini in another, and the amounts of both in yet one more. That final batch turned out perfectly! The muffins rose nicely and had beautiful bakery-style domed tops, their insides were soft and moist (without looking or tasting raw!), and you could still taste the zucchini in every bite.
Therefore, the moral of this (vegetable) story is… Stick with the amount of zucchini in the Ingredients list, do not try adding any extra, and fully dry it first!
HOW TO MAKE THE BEST HEALTHY ZUCCHINI MUFFINS
Now that you have all of your ingredients, let’s talk about how to make these zucchini muffins. It’s a simple recipe, but I still have some tips for you to make sure your muffins turn out beautifully! We’ll start with the most important one first, which I just alluded to a moment ago, and that’s…
Thoroughly dry the zucchini. This is extremely important. Zucchini contains a lot of moisture, which it releases into the batter as the muffins bake. That extra moisture will ruin the structure of your muffins, cause them to collapse, and make the insides much too wet.
To combat that, you’ll dry your zucchini before adding it to the batter. That’s really easy to do! Spread your freshly grated zucchini out over a double-thick layer of paper towels. Use a second double-thick layer to press down on top of the zucchini. Be firm and press as hard as you can! You want to soak up as much liquid as possible so the insides of your muffins are soft and the tops are tall and domed.
Tip: I generally use two sets of double-thick paper towels to be very thorough. I also press out the zucchini’s moisture first, before I start measuring any of the other ingredients, so I’m sure it’s dry by the time I’m ready to add it to the batter.
Stir by hand — and gently. Put away your hand-held and stand mixers! These tend to over-mix batters that have very little fat (like this one!), and over-mixing creates a tough or gummy texture. For perfectly soft and tender muffins, use a whisk where explicitly instructed, and use a fork for everything else.
Why a fork? And not a spatula or wooden spoon?
Unlike with a spatula or spoon and their flat surfaces, ingredients can pass through the open space between the tines of the fork as you stir. Therefore, it’s more efficient and generally means you end up stirring less — which also helps guard against over-mixing!
When you add the zucchini to your bowl, gently fold it in. (I still use a fork to do this!) I know it’s tempting to rush through mixing in the zucchini so you can get your muffins in the oven and eat them that much sooner, but they won’t be as soft and tender. I promise the gentle stirring is worth it!
Coat the liners. Whether you use paper liners like I did or dollop the batter directly into the cups of your muffin pan, generously coat them with nonstick cooking spray. Low fat batters (like this one!) tend to stick to liners like superglue, but covering them with cooking spray first helps the liners peel away more easily — or, if you skipped the liners, it helps the muffins pop right out of the pan!
Tip: If you forget or just weren’t generous enough with the cooking spray, then tightly seal your muffins inside of an airtight container or zip-topped bag, and refrigerate them overnight. I’ve found this trick helps loosen the liners, especially if you try to peel them away when the muffins are cold!
Bake. An obvious final step! 😉 Your zucchini muffins will be done when the tops feel firm and a toothpick inserted into the center comes out clean or with fully baked crumbs attached.
FAQS ABOUT HEALTHY ZUCCHINI MUFFINS
Are these healthy zucchini muffins sugar free, gluten free, low calorie, or clean eating?
Yes — to all of the above! They’re naturally sugar free, low calorie, and clean eating. I’ve included recommendations about how to make them gluten free in the Notes section of the recipe too.
Can I use whole eggs?
You sure can! I’ve shared how to modify the wet ingredients if you’d like to use whole eggs in the Notes section as well.
I don’t have that sweetener. What can I substitute instead?
There are a few different options! I’ve included them in the Notes section for you too.
Can I add more zucchini to the batter?
Please don’t — I beg you! It’ll make your muffins collapse, and the insides will be rather wet. See the “Zucchini” header in the “Ingredients” section above for more information!
What’s the best way to store these zucchini muffins? And how long do they last?
Store them in an airtight container in the refrigerator. They should last at least four days, if not longer!
Can I freeze these zucchini muffins?
Absolutely! These freeze really well. I like to thaw individual muffins in the microwave on 50% power until they’re warmed all the way through. They almost taste freshly baked like that!
Tip: If using paper liners, I recommend removing them before freezing. (It’s harder to peel them off after thawing or reheating the muffins!)
And just like that… Breakfast is freshly baked and served! Then when you make your own, remember to snap a picture and share it on Instagram using #amyshealthybaking and tagging @amyshealthybaking IN the photo itself! (That guarantees I’ll see your picture! 🙂 ) I’d love to see your healthy zucchini muffins!

The Ultimate Healthy Zucchini Muffins
Ingredients
- 2 ¼ cups (270g) white whole wheat flour or gluten free* flour (measured like this)
- 1 tbsp (7g) ground cinnamon
- ½ tsp ground allspice
- ¼ tsp ground nutmeg
- 1 ½ tsp baking powder
- ¾ tsp baking soda
- ¼ tsp salt
- ½ tbsp (7g) unsalted butter or coconut oil, melted and cooled slightly
- 2 large egg whites, room temperature
- 1 tbsp (15mL) vanilla extract
- 2 ½ tsp liquid stevia (see Notes!)
- ½ cup (120g) plain nonfat Greek yogurt
- ¾ cup + 2 tbsp (210mL) nonfat milk, divided
- 1 ½ cups (135g) freshly grated zucchini, thoroughly patted dry (see Notes!)
Instructions
- Preheat the oven to 350°F, and coat 12 muffin cups with nonstick cooking spray. (If using liners, then line 12 muffins cups with liners and coat them with cooking spray.)
- In a medium bowl, whisk together the flour, cinnamon, allspice, nutmeg, baking powder, baking soda, and salt. In a separate bowl, whisk together the butter or coconut oil, egg whites, vanilla extract, and liquid stevia. Add in the Greek yogurt, stirring until no large lumps remain. Stir in 6 tablespoons of milk. Alternate between adding the flour mixture and remaining milk, beginning and ending with the flour mixture, and stirring just until incorporated. (For best results, add the flour mixture in 3 equal parts.) Gently fold in the zucchini.
- Divide the batter between the prepared muffin cups. Bake at 350°F for 30-34 minutes or until the top feels firm to the touch and a toothpick inserted into the center comes out clean (or with a few crumbs attached). Cool in the pan for 5 minutes before transferring to a wire rack to cool completely.
Notes
View Nutrition Information + Weight Watchers Points
You may also like Amy’s other recipes…
♡ Healthy Zucchini Oatmeal Muffins
♡ The Ultimate Healthy Zucchini Bread
♡ Healthy Zucchini Oatmeal Snack Cake
♡ Healthy Chocolate Chip Zucchini Oatmeal Breakfast Cookies
♡ The Ultimate Healthy Apple Muffins
♡ The Ultimate Healthy Blueberry Muffins
♡ Healthy Carrot Cake Oatmeal Muffins
♡ …and the rest of Amy’s healthy muffin recipes and healthy zucchini recipes!
There really is something special about muffins. I also remember as a kid getting muffins while traveling somewhere and it was like a treat. This post also makes me want to go to Disney ASAP. I was reading another blog recently about her families Disney recap and my soul feels the call. I’d pack an entire tray of these muffins for full energy at the park. LOL
Oh man… If you went to Disneyland again, I’d totally meet up with you there, Brittany!! I’d bring an entire batch of these muffins just for you. Along with any other baked goodies you’d like too, of course! 😉 I can’t wait for the day where we FINALLY get to meet in person!! ♡