Made with vegetable puree and shredded cheese, this cheese quesadilla tastes just as good as a classic quesadilla, yet it packs in a serving of veggies. These Healthier Cheese Quesadillas are perfect for toddlers, picky kids, and even adults!

A "Healthy" Quesadilla
This is not your average cheese quesadilla.
Instead of a single layer of gooey cheese, there is a vegetable tucked into the layer of cheese that is nearly undetected.
Orange vegetables, like carrots, butternut squash, sweet potatoes, and pumpkin, are naturally sweet and pair beautifully with sharp cheddar cheese.
After cooked, they can easily be turned into a velvety, smooth puree that can work to add sweetness to recipes like Bean Burritos, Spaghetti Sauce, or Cheese Quesadillas. In fact, the vegetable puree goes nearly undetected.
Disclaimer: That said, I do believe in letting your family know there are vegetables in their meals, so they realize not only the importance of eating vegetables, but they realize they actually enjoy eating them.
Back to the quesadillas, instead of copious amounts of cheese to make the quesadilla gooey, a thin layer of vegetable puree is topped with shredded cheddar and then toasted or heated to make a cheesy quesadilla with added nutrients.
These healthier cheese quesadillas are one of my all-time favorite quick lunches to feed my picky kids.
Key Ingredients
- Tortillas: Use any tortilla you like. Homemade tortillas, store-bought or gluten-free.
- Cheese: Sharp cheddar is best, as the color and flavor help to mask the vegetables. It is also best to shred the cheese yourself for the cheese to melt uniformly. Pre-grated cheese is coated with anti-caking agents.
- Vegetable Puree: Butternut squash puree is mild and perfect for these quesadillas. I often use Instant Pot Butternut Squash as the base, as it comes together effortlessly and can be stored in the freezer to use as desired. However, feel free to use canned or homemade pumpkin puree, sweet potato puree, or carrot puree. Even a jar of baby food works perfectly.
How to Make Cheese Quesadillas with Vegetable Puree
- Spread one tortilla with a thin layer of vegetable puree.
- Top with an even layer of shredded cheese.
- Cover with another tortilla.
- Cook quesadilla either on a griddle or in the microwave.
- For a Crispy Quesadilla: Lightly grease a nonstick skillet. Heat over medium heat, and toast the quesadilla for 2-3 minutes per side, or until the cheese is melted. Microwave on high for 45 seconds. Let cool and then cut into wedges.
- For a Soft Quesadilla: Place the quesadilla on a heat-safe dish and cover with a slightly damp paper towel to keep the tortilla from drying out. Microwave on high for 45 seconds. Let cool and then cut into wedges.

More Kid-Friendly Veggie Recipes
- Baked Vegetable Egg Rolls
- Ranch Veggie Wrap
- Easy Bean Burritos with Hidden Veggies
- Sweet Potato Waffles
- Maple Glazed Carrots
I would love to hear if you enjoyed these quesadillas! Leave a comment and review below.

Cheese Quesadilla with Butternut Squash
Ingredients
- 1 cup Butternut Squash Puree
- 4 ounces sharp cheddar cheese shredded
- 8 tortillas
Instructions
- Spread 4 tortillas with a thin layer of squash puree. Sprinkle an even layer of cheese over each tortilla. Top with the remaining tortillas.
- For a crispy quesadilla, grease a nonstick skillet and heat over medium heat. Once heated, add the prepared quesadilla, one at a time, and heat 2-3 minutes per side until the cheese is melted. Repeat with the remaining quesadillas.
- For a soft quesadilla, place a single prepared quesadilla onto a heat-safe plate and cover with a lightly damp paper towel. Microwave for 45 seconds, or until the cheese is melted through. Repeat with the remaining quesadillas.
- Let the quesadillas cool and then cut into wedges and serve.
Notes
- Instead of Butternut Squash Puree, you can use sweet potato puree, carrot puree, or even 100% canned pumpkin.
Natalie
Nice, just what I was looking for. I have puree in my fridge. I will make this tomorrow for lunch. Thanks!
Hanna
This is a great idea! I agree, let them know vegetables are delicious too! Why are kids so picky!?!
Meagen Brosius
I love making recipes like this to help the kids get extra veggies! Such a great idea and a delicious recipe!
Kristen Chidsey
Thanks so much Meagan! It is a great way to enjoy veggies for sure!
Jenn
Looooove the cheesy butternut pairing in these quesadillas! Totally tasty!
Kristen Chidsey
It is surprising how much the butternut squash pairs well with the squash. So glad you enjoyed Jenn!
melissa @ treats with a twist
What a fun idea for kiddos (or husbands)!! Love this!
Kristen Chidsey
Yes, fun for husbands and kids for sure Melissa!
Shashi at RunninSrilankan
Kristen, my daughter and your daughter would have so much to share about their EPIC love of cheese and crackers!
By the way - speaking of EPIC - WOW - I so so love your use of butternut squash puree in these quesadillas - it's an EPICALLY brilliant idea! I cannot wait to try this - Walmart sells those bags of diced butternut squash and I have 2 bags in my fridge - think I'm gonna roast 'em up and try this this afternoon - thanks so much friend! And I hope your weekend is wonderful xoxo
Kristen Chidsey
I think your daughter and my daughter would probably make pretty epic friends as well!
Katie | Healthy Seasonal Recipes
Great idea to bake the butternut squash whole and then cut it! My kids love quesadillas. This would be a hit in my house!!
Kristen Chidsey
Yes, I bet they would be!
Rachel @ Baked by Rachel
This is such a great idea for a quick lunch!
Kristen Chidsey
Thanks Rachel!
Sarah
Ooh yes - hello lunch! I've got a huge butternut squash sitting on my counter begging to be used and this sounds perfect!
Kristen Chidsey
Yes, this would be a great way to use it up!