This Healthy Zucchini Tomato Bake recipe is an easy way to use up all your summer vegetables. Fresh, healthy and full of flavor- it’s the perfect side dish!

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Is there anything better than sweet tomatoes, fresh zucchini and melty cheese? Nope! And this Healthy Zucchini Tomato Bake is just that!
This low carb veggie side dish is easy, delicious and quick to make!

Years ago Tyler’s mom made a variation of this Healthy Zucchini Tomato Bake and I’ve loved it as a side dish ever since!
why we love this Zucchini Tomato Bake
This zucchini tomato bake is the perfect way to use up summer produce. Here’s why we love it:
- Easy to make: This recipe is super easy to make. Slice zucchini and tomatoes, layer them in a dish and top with a delicious olive oil cheese mixture
- Simple Ingredients: This recipe is made with only 6 simple ingredients that you probably already have on hand!
- Best way to use summer produce: This recipe really lets fresh zucchini and tomatoes shine! For another tomato recipe, try our Homemade Tomato Sauce!
We always have an abundance of squash and tomatoes, and it’s so quick to slice them up and bake them with a little bit of parmesan cheese!
If you’re looking for other healthy zucchini recipes – check out this Zucchini Bread, Zucchini Lasagna, or these 30 Healthy Zucchini Recipes!
Healthy Zucchini Bake Items:
To make this zucchini tomato bake you’ll need the following:
- Glass baking dish
- Olive oil
- Parmesan Cheese
- Zucchini
- Tomatoes
- salt and pepper

You can find substitutions for all of these ingredients below in the green shaded substitutions box.
Truthfully this is one of the easiest dishes that you will ever make.
How to make Healthy Zucchini Tomato Bake:
This vegetable bake is SO easy to make.
- First – slice your zucchini + tomatoes about 1/4 inch thick.
- Then, layer zucchini + tomatoes in a pan. You can make a pattern like I did, or just toss them in there!
- Mix together your parmesan cheese, olive oil and herbs.
- Drizzle over veggies.
- Bake in the oven and you’re done!
It’s seriously so delicious and simple!




If your garden is over flowing, you just need a quick summer side dish, or you’re looking for an easy way to get in veggies this winter – this Healthy Zucchini Tomato Bake recipe for you!
What to Serve with Zucchini Tomato Bake:
This recipe is so versatile, it really goes with anything! Here are our favorite things to serve with this zucchini bake:
- Pineapple Grilled Chicken
- Balsamic Grilled Chicken
- Vegetable Primavera Pasta
- Crockpot Whole Chicken
- Best Baked Boneless Chicken Breast
Substitutions for zucchini tomato casserole recipe:
Veggies: You can use all green or all yellow squash in this recipe. You can also add chopped onion.
Chopped Veggies: You can chop all of the vegetables in pieces and mix them up in a bowl if you don’t want to arrange them. Chop in 1 inch cubes.
Fresh Basil: If you don’t have fresh basil, you can substitute 1/2 tablespoon dried basil
Oil: Olive oil is the best option for this recipe, but avocado oil will also work!
Mozzarella: We like to add 1/4 cup shredded mozzarella to this recipe for even more cheesiness!
Vegan: To make this vegan use vegan parmesan, or omit cheese completely
Breadcrumbs: This is delicious with 1/8 cup of panko breadcrumbs sprinkled on top!

Storing & Serving Zucchini Bake:
Making ahead: You can make this up to 24 hours in advance and bake when you’re ready to eat.
Storing: You can store this in the refrigerator for up to 5 days
Freezing: We don’t recommend freezing this dish. Frozen veggies can get very watery.
Zucchini Tomato Bake FAQ
The key to cooking zucchini so that it doesn’t get soggy is to not over cook it! Zucchini goes from being firm and delicious to a ball of mush in a matter of minutes!
Pretty much anything goes well with zucchini! It’s a very neutral vegetable. I like too serve this with Crockpot Shredded Chicken or Healthy Pulled Pork.
When cooking zucchini, make sure you watch it closely towards the end. It cooks very fast. The best thing to do is set a timer!
It’s easy to bake zucchini and tomatoes! Slice into 1/4 inch thick slices, layer in a glass baking dish and bake at 350 for 20 minutes.
Other healthy side dish recipes:
Check out these other healthy side dish recipes!

Healthy Zucchini Tomato Bake
Ingredients
- 1 cup zucchini sliced
- 1 cup yellow squash sliced
- 2 cups tomatoes sliced
- 2 tablespoons basil fresh, chopped
- 2 tablespoons olive oil
- 1/4 cup grated Parmesan cheese
- 1/2 teaspoon salt
- 1/2 teaspoon pepper
Instructions
- Preheat oven to 350 and spray a pie dish or 8×8 baking dish with oil
- Slice the tomato and squash into 1/4 inch thick slices.
- Layer the squash and tomato in a pattern, side by side until the pan is full
- Whisk together chopped basil, olive oil, salt, pepper and Parmesan cheese. Pour it over vegetable mixture until covered.
- Bake at 350 for 20-25 minutes until vegetables are slightly tender. If you like your vegetables cooked well, keep the dish in the oven for an extra 5-10 minutes.
- Optional: Top with additional parmesan and optional hot pepper flakes
Video
Notes
- You can use all green or all yellow squash in this recipe
- You can chop all of the vegetables in pieces and mix them up in a bowl if you don’t want to arrange them. Chop in 1 inch cubes.
Myra says
That looks so good!!! Zucchini is my fave and I have a ton of fresh basil to use up from the garden 🙂
The Clean Eating Couple says
Thank you!! I looove zucchini + tomatoes together
GiGi Eats says
Mmmmmmm Zucchini and Tomatoes = YUMM!
The Clean Eating Couple says
Right?! Best combo!
Cassie says
I’ll sub the Parmesan cheese for nutritional yeast, but otherwise this bake looks so delectable! All of my favorite vegetables in one!
The Clean Eating Couple says
Good idea! I have some nutritional yeast that I haven’t tried yet – I have to do that!
Kaitlin @ California Endless Summer says
Such a good idea to put these together!
The Clean Eating Couple says
Thank you! They’re some of my favorite ingredients!
Roshani Khanna says
Delicious! This will be the perfect treat for those hot days & nights that are around the corner. Love it!
The Clean Eating Couple says
Yes! It’s great for summer dinners!
S davis says
Cook time was not long enough, other than that wonderful!
The Clean Eating Couple says
Hi Steffanie – You may have not sliced the tomatoes/squash as thin as necessary for it to cook in time. But regardless – I’m glad you liked it!
Carol says
I make a recipe like this often, love it. I usually chop veggies in I inch chunks, use a variety of cherry tomatoes and lots of garlic. .I look forward to the leftovers the next day by mixing them into pasta. So delicious. Save a little pasta water to add.
The Clean Eating Couple says
That’s a great idea to use the leftovers over pasta! Yum!!
Janice says
So much flavor and so easy to prepare! Made this tonight and will be making it again. Thank you for sharing the recipe.
The Clean Eating Couple says
So glad you like it, Janice!! It’s one of my favorites too 🙂 Leftovers are great cut up over pasta – yum!!
Linda says
This recipes is not only easy but so delicious! It’s also got a beautiful presentation if you were entertaining guests. I have made this for Christmas Eve the last few years as I have a couple of family members that are gluten intolerant . This is a perfect dish for any occasion!
The Clean Eating Couple says
Yay! Makes me so happy to hear this 🙂
Rachel Locey says
Delicious. I cut the squash and zucchini into chunks & used cherry tomatoes cut in half. Fresh basil can be hard to find, so I used chopped frozen basil (found it in the freezer section; looks like ice cubes). I prefer less oil; this was good with about half the oil, in my opinion.
I will definitely make it again.
The Clean Eating Couple says
So glad you liked it!! Thanks, Rachel!
Jessica says
It came out delicious, I will definitely be making this more throughout the summer!
The Clean Eating Couple says
Glad you liked it, Jessica! Thank you so much!
Madison says
Love this for a summer side dish!! We added mozzarella as suggested and it was delicious!
The Clean Eating Couple says
So glad you liked it, Madison! Thank you!
Wendy Geoghan says
Absolutely delicious! I had tomatoes and zucchini that I wanted to use. Had all the ingredients at home. I cut the recipe in half, only two of us. Followed directions and this dish looked great and tasted wonderful. And healthy! Will definitely make it again.
The Clean Eating Couple says
So glad you liked it, Wendy! Thank you so much!
Joanne says
This was so easy and delicious I have made it 3 times in the last month!!
The Clean Eating Couple says
Love hearing that, Joanne! It’s my favorite summer side dish!
Rita T Yusko says
In the photo – did you use spinach in this dish? Looks like more than 2 Tbs. basil.
The Clean Eating Couple says
No I didn’t. It’s made exactly as the recipe is written – although I’m sure spinach would be a great addition!
Cara says
This was AMAZING. Used my own seasoning choice. Made today for Thanksgiving.
The Clean Eating Couple says
So happy you enjoyed it, Cara! Thank you!
Leslie Poff says
This is what I’ve needed to stop over baking my zucchini 🙈 I added some feta cheese and a bit of Cajun seasoning for a kick and it was fantastic! Will definitely be making it again! 💕
The Clean Eating Couple says
Love that combo!! Sounds great!
Amy Jo says
This was an easy, quick, and tasty dish. And it’s healthy too! I can’t eat Parmesan cheese (weird reaction to certain cheeses), so I used about a half cup of mozzarella cheese in the mix instead then put parm out for others to sprinkle on at the table. Everyone enjoyed it, even my hubby who is not a big fan of zucchini and summer squash.
The Clean Eating Couple says
So happy you enjoyed it!
Janet says
Have made this numerous times, varied with what I have. Add thinly sliced white onion, use mixed dried Italian or middle east spices. Your choice!
Use shredded mozza at end (just to melt it( if you don’t wantparmigan.
Check out Briam recipes to add thinly sliced potatoes. Your ‘sides’ are done!
The Clean Eating Couple says
So glad you liked it!
Eva Herrera says
Love this recipe. Very healthy!
Please send me the free recipe book.
Thank
Lisa says
This was so tasty and a great use of fresh produce! Only changes I would make are adding some sliced garlic in the layers and finish with a topping of fresh basil to serve. But it was filling and delicious! Will definitely make it again.
Kathy Miller says
Was a wonderful recipe and will be made in our house again.
AUT says
Could I use green tomatoes maybe?
The Clean Eating Couple says
I’m not sure. they’re a different flavor and less sweet so I’m not sure how it would work. Sorry!
Ann graves says
Sounds good
Bernadette says
This dish was delicious! I did add 1 tsp of Italian seasonings for even more flavor.
PJ says
Even though I used exact measurements, I feel like it could’ve used more of the mixture as it only covered some of the top layer. I may give it another try.
The Clean Eating Couple says
Did you use the right size dish? Not sure what you mean here by ‘top layer’
PJ says
Yes I used a pie dish. And I overlapped the squash and tomatoes a little. There wasn’t enough mixture to cover everything but I’ll give it another try!
The Clean Eating Couple says
There shouldn’t be two layers, just one to fill the dish!
George Medina says
Outstanding dish! Great for using the extra tomatoes and zucchini from my garden.
Virginia says
This was delicious! I chopped the zucchini and used chopped grape tomatoes because that’s what I had. It was a great side dish to pork chops – very summery.
Barb says
This turned out to be very “watery”