Healthy Zucchini Tomato Bake

Published by:
Liz Marino
| 04/22/2022 | Last Updated: 06/25/2025

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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!

An overheat shot of Healthy Zucchini Tomato Bake in a cast iron skillet


 

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

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!

We always have an abundance of squash and tomatoes in the summer, and it’s so quick to slice them up, layer them in a dish, and bake them with a little bit of parmesan cheese!

It’s made with only 6 simple ingredients and allows the summer veggies to shine! For another tomato recipe, try our Tomato Sauce with Fresh Tomatoes.

If you’re looking for other healthy zucchini recipes – check out this Zucchini Bread, Zucchini Lasagna, or these 30 Healthy Zucchini Recipes!

tyler’s top tip for zucchini tomato bake

  • The key to cooking zucchini so that it doesn’t get soggy is not to overcook it! Zucchini goes from being firm and delicious to a ball of mush in a matter of minutes!
  • When cooking zucchini, make sure you watch it closely towards the end. It cooks very fast. The best thing to do is to set a timer!

Ingredients

Ingredients of Zucchini Tomato Bake Casserole in small white bowls on a grey background

Substitutions

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 cheese to this recipe for even more cheesiness!

Vegan: To make this vegan use vegan parmesan, or omit cheese completely

Bread crumbs: This is delicious with 1/8 cup of panko breadcrumbs sprinkled on top!

How to make Healthy Zucchini Tomato Bake:

Zucchini, squash and tomatoes in a cast iron skillet before baking
  1. First – slice your zucchini + tomatoes about 1/4 inch thick. Then, layer them in a pan. You can make a pattern like I did, or just toss them in there!
Herbs, olive oil and cheese being mixed together to be poured on top of zucchini bake
  1. Stir together your parmesan cheese, olive oil and herbs.
Zucchini Tomato Bake before being put in the oven
  1. Sprinkle over veggies.
A close up of Zucchini Bake in a pan fresh out of the oven.
  1. 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:

a spoon taking a scoop out of zucchini bake

Storing:

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.

A close up of Zucchini Tomato Bake in a cast iron skillet
An overheat shot of Healthy Zucchini Tomato Bake in a cast iron skillet

Healthy Zucchini Tomato Bake

Recipe by: Liz Marino
4.56 from 49 votes
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!
Prep Time : 5 minutes
Cook Time : 25 minutes
Total Time : 30 minutes
Serves : 6 servings
(hover over # to adjust)

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 black pepper

Instructions

  1. Preheat oven to 350 and spray a pie dish or 8×8 baking dish with oil
  2. Slice the tomato and squash into 1/4 inch thick slices.
  3. Layer the squash and tomato in a pattern, side by side until the pan is full
  4. Whisk together chopped basil, olive oil, salt, pepper and Parmesan cheese. Pour it over vegetable mixture until covered.
  5. 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. 
  6. Optional: Top with additional parmesan and optional hot pepper flakes

Notes

Substitutions for this recipe:
  • 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. 

Nutrition Facts

Serving: 1cup | Calories: 75kcal | Carbohydrates: 4g | Protein: 3g | Fat: 6g | Saturated Fat: 1g | Cholesterol: 4mg | Sodium: 262mg | Potassium: 230mg | Fiber: 1g | Sugar: 2g | Vitamin A: 565IU | Vitamin C: 14mg | Calcium: 59mg | Iron: 1mg
Course: Side Dish
Cuisine: American
Tried this recipe?Share it! Make sure to tag @thecleaneatingcouple or use #thecleaneatingcouple!
4.56 from 49 votes (25 ratings without comment)

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Recipe Rating




53 Comments

  1. Bernadette says:

    5 stars
    This dish was delicious! I did add 1 tsp of Italian seasonings for even more flavor.

  2. Could I use green tomatoes maybe?

    1. 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!

  3. Kathy Miller says:

    5 stars
    Was a wonderful recipe and will be made in our house again.

  4. 5 stars
    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.

  5. Eva Herrera says:

    5 stars
    Love this recipe. Very healthy!

    Please send me the free recipe book.

    Thank

  6. 5 stars
    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!

    1. The Clean Eating Couple says:

      So glad you liked it!

  7. 5 stars
    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.

    1. The Clean Eating Couple says:

      So happy you enjoyed it!

  8. 5 stars
    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! 💕

    1. The Clean Eating Couple says:

      Love that combo!! Sounds great!

  9. 5 stars
    This was AMAZING. Used my own seasoning choice. Made today for Thanksgiving.

    1. The Clean Eating Couple says:

      So happy you enjoyed it, Cara! Thank you!

  10. Rita T Yusko says:

    In the photo – did you use spinach in this dish? Looks like more than 2 Tbs. basil.

    1. 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!

  11. 5 stars
    This was so easy and delicious I have made it 3 times in the last month!!

    1. The Clean Eating Couple says:

      Love hearing that, Joanne! It’s my favorite summer side dish!

  12. Wendy Geoghan says:

    5 stars
    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.

    1. The Clean Eating Couple says:

      So glad you liked it, Wendy! Thank you so much!

  13. 5 stars
    Love this for a summer side dish!! We added mozzarella as suggested and it was delicious!

    1. The Clean Eating Couple says:

      So glad you liked it, Madison! Thank you!

  14. 5 stars
    It came out delicious, I will definitely be making this more throughout the summer!

    1. The Clean Eating Couple says:

      Glad you liked it, Jessica! Thank you so much!

  15. Rachel Locey says:

    5 stars
    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.

    1. The Clean Eating Couple says:

      So glad you liked it!! Thanks, Rachel!

  16. 5 stars
    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!

    1. The Clean Eating Couple says:

      Yay! Makes me so happy to hear this 🙂

  17. 5 stars
    So much flavor and so easy to prepare! Made this tonight and will be making it again. Thank you for sharing the recipe.

    1. 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!!

  18. 5 stars
    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.

    1. The Clean Eating Couple says:

      That’s a great idea to use the leftovers over pasta! Yum!!

  19. 5 stars
    Cook time was not long enough, other than that wonderful!

    1. 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!

  20. Roshani Khanna says:

    5 stars
    Delicious! This will be the perfect treat for those hot days & nights that are around the corner. Love it!

    1. The Clean Eating Couple says:

      Yes! It’s great for summer dinners!

  21. Kaitlin @ California Endless Summer says:

    Such a good idea to put these together!

    1. The Clean Eating Couple says:

      Thank you! They’re some of my favorite ingredients!

  22. I’ll sub the Parmesan cheese for nutritional yeast, but otherwise this bake looks so delectable! All of my favorite vegetables in one!

    1. The Clean Eating Couple says:

      Good idea! I have some nutritional yeast that I haven’t tried yet – I have to do that!

  23. GiGi Eats says:

    Mmmmmmm Zucchini and Tomatoes = YUMM!

    1. The Clean Eating Couple says:

      Right?! Best combo!

  24. 5 stars
    That looks so good!!! Zucchini is my fave and I have a ton of fresh basil to use up from the garden 🙂

    1. The Clean Eating Couple says:

      Thank you!! I looove zucchini + tomatoes together