Zucchini Stuffed Shells With Cottage Cheese

These zucchini-stuffed shells are a hearty vegetarian dinner option. Baked in a 9×13 baking dish, smothered with a rich marinara sauce, melty mozzarella cheese, creamy cottage cheese, fresh spinach, and Italian seasoning, you’re going to want seconds. The jumbo pasta shells are cooked until just al dente so they hold their shape, then stuffed with a cheesy vegetable mixture that bakes into bubbling comfort food. Perfect for family meals, this Italian-American classic gets a fresh twist from summer fresh zucchini and yellow squash, making it the ideal way to use up summer produce as the weather cools down.

I wanted to try something new with zucchini this year. As the evenings turned more fall-like, the idea of combining garden vegetables with a cozy baked pasta casserole just felt right. These zucchini-stuffed shells bring together the best of both worlds: bright, garden zucchini folded into the kind of cheesy, saucy comfort food that feels right at home as September nights start cooling off.

Suppose you’re in the mood for more crossover dishes. In that case, my layered zucchini tomato casserole is another way to cook with summer squash. 

Why You Will Love This Stuffed Pasta Shell Recipe With Zucchini

Seasonal meets comfort – It uses up garden zucchini and yellow squash. Still, it bakes into the kind of cheesy, saucy comfort food everyone craves once the evenings turn cool.

Impressive but straightforward – Jumbo shells stuffed with cottage cheese, spinach, and veggies look like a special occasion dish. Still, the prep is straightforward enough for a weeknight using just one large pot and a large bowl.

Make-ahead friendly – You can assemble the whole thing in the morning and pop it in the oven at dinnertime without stress.

Why Stuffed Shells Feel Right at Home in Canadian Kitchens

In Canadian kitchens, stuffed pasta dishes like this often show up at family gatherings, church suppers, and potluck dinners. They’ve become a comfort food staple not just because of their Italian roots, but because they fit so well into the way we cook here: hearty casseroles baked in a 9×13 dish, ready to serve a crowd. Using zucchini and yellow squash adds a distinctly Canadian seasonal touch, since these vegetables overflow from late-summer gardens and farmers’ markets across the country.

Where I grew up, there was a heavy Italian population, many of whom had come to work in the local steel mill. By the 1980s, the Italian influence on food was so strong that there was a running joke when you went out to eat: “What do you want—Italian food, or Italian food?” It speaks to how seamlessly these recipes worked their way into our community tables, becoming just as Canadian as they were Italian. Sometimes the filling was a classic ricotta mixture, other times cottage cheese stood in — both worked beautifully.

This zucchini stuffed shells recipe is my way of carrying that tradition forward, blending garden vegetables with the comfort of a bubbling baked pasta.

Let’s Get Started Making These Stuffed Jumbo Shells

You can start cooking the shells in a large pot of salted water until they are just al dente, and then begin preparing the filling. 

Start by peeling, washing, and dicing the zucchini and yellow squash into the smallest pieces you can manage—the smaller the dice, the better they’ll meld into the filling. Mince the fresh spinach and don’t skip mincing the garlic either; it’s an absolute must for flavor, but big pieces will be noticeable.

Once the pasta is done, drain it under cold water in a colander and rinse with cold water to make it easier to handle for filling.

In a large bowl, stir together the diced vegetable mixture, spinach, garlic, cottage cheese, and Italian seasoning. I used 2% cottage cheese here—it’s creamy without being too heavy.

For the tomato sauce, go with something rich and tomato-forward. A good homemade marinara sauce with basil and oregano works well, or you can opt for a thick, jarred marinara sauce from the store. Thin sauces won’t do you any favors, since the raw vegetables will release liquid as they cook. Just watch if you choose a spiced tomato sauce, balance the Italian seasoning with the herbs in the sauce.

Take a spoon and fill each cooled pasta shell with the filling, then arrange them in a 9×13 baking dish. Spoon tomato sauce generously over the top, so every shell is well-covered.

Follow the rich tomato sauce up with a three tablespoon of snipped fresh chives for a milder onion flavor.

Next, grate three cups of pizza mozzarella and sprinkle it evenly over the entire surface. The brick-style mozzarella melts better than pre-shredded, and it’s easy enough to grate yourself. Give the top a light shake of Italian seasoning for good measure.

Bake the casserole uncovered at 400°F for 30 minutes, then switch to broil on high heat for 2–3 minutes until the cheese is browned and bubbling. Let it sit for a few minutes before serving so everything sets up just right. That’s it—straightforward, hearty, and dinner’s done.

Ingredients:

Note to my Canadian readers: You’re not alone if you’re sourcing these ingredients without relying on U.S.-based imports. Given our country’s current challenges, supporting Canadian-owned businesses and Canadian-made products matters more than ever. Every little bit helps keep our food systems strong, our neighbors employed, and our dollars in our communities.

You will now find more Canadian content on the blog as I continue to source Canadian food brands and products. 

And to our American friends—we still love you! We always have and will. But when possible, we’re leaning toward local to keep our shelves stocked and our people supported.

Jumbo pasta shells – Big enough to hold a hearty scoop of filling and sturdy enough to bake without falling apart; cook until al dente. Italpasta makes an outstanding Jumbo shell.

Zucchini and yellow squash – Mild, fresh vegetables that add moisture and sneak in extra nutrition; dicing small helps them blend seamlessly. A farmer’s market, local gardens, and fresh summer produce are best. Try to use a smaller zucchini as it will have fewer seeds. You can also cut the seeds from the flesh if using a larger zucchini and discard them.

Fresh spinach – Minced spinach gives a pop of color and a boost of vitamins while staying mild in flavor. Buying local greens is even better — they reach your kitchen faster after harvest, which means they retain more nutritional value and have a fresher taste.

2% cottage cheese – Creamy, high-protein, and lighter than ricotta, but still gives the filling that classic stuffed shell texture. Chances are, if you live in Ontario, you know already who I am recommending for Cottage cheese. You guessed right, it’s Nordica!

Fresh garlic – Brings bold, savory flavor that keeps the filling from tasting flat; it’s a must-have here. I am lucky my father-in-law loves growing a new crop of garlic every year, so I always have a fresh supply. When you’re unsure, check the market or local roadside stands in Ontario during August. 

Italian seasoning – A ready-made blend that delivers balanced herbs in every bite.

Rich marinara sauce – A thick tomato-based or marinara sauce helps keep the casserole from turning watery and adds depth of flavor.

Fresh Chives – I used these to give the dish a bit of onion flavor without overpowering the dish.

Pizza mozzarella – Grated from a brick, you’ll want at least 1 cup of mozzarella for full coverage; it melts into gooey, stretchy cheese that browns beautifully under the broiler. I used Galbani light pizza mozzarella for this recipe. 

Substitutions and Add-Ins For This Savory Italian-Style Summer Squash Pasta

Jumbo pasta shells: If you can’t find the big shells, use manicotti tubes instead. They’ll hold the same filling and bake up just as well.

Zucchini and yellow squash – Swap in diced pattypan squash if you’re out. It has the same mild flavor and texture, blending seamlessly into the filling.

Fresh spinach – Frozen chopped spinach works fine; thaw it and squeeze out all the water so the filling doesn’t get soggy. Kale, chard, or even beet greens can be used as a substitute if that’s what’s available in the fridge.

2% cottage cheese – I like using cottage cheese here for a lighter, high-protein filling. For a richer meal, consider using ricotta or a blend of ricotta and cream cheese.

Fresh garlic – Garlic powder can work in a pinch, but fresh minced garlic gives the sharp bite that makes the filling come alive.

Italian seasoning – No blend on hand? Mix dried basil, oregano, thyme, and a small amount of rosemary. Fresh basil works beautifully if you’ve got it.

Rich marinara sauce – Any thick tomato sauce works, but you can switch to tomato basil, arrabbiata for heat, or even a homemade sauce with garden tomatoes if you’ve got the time.

Pizza mozzarella – Use regular mozzarella, provolone, or a blend of melty cheeses. Grated cheddar or Monterey Jack will give a sharper twist, though they brown faster under the broiler.

Vegetable variations – If you’d like to reduce the squash or stretch the filling, opt for other soft vegetables that blend in effortlessly. Diced eggplant, pattypan squash, or even a little sautéed leek work well alongside zucchini without changing the flavor balance.

Expert Tips, Serving and Storing Suggestions for This Cheesy Zucchini Stuffed Pasta Dish

Tip #1: Drain those veggies well. Zucchini and yellow squash carry a lot of water. Dice them small, add salt if needed, and blot with a paper towel or press out excess liquid to prevent your filling from becoming watery in the oven.

Tip #2: Use brick mozzarella, not pre-shredded. Grating a block of pizza mozzarella only takes a minute, and it melts creamier and browns better. Pre-shredded cheese is coated in starch, which can cause the topping to become clumpy.

Tip #3: Bake uncovered for the right finish. Covering the pan will steam the shells. Leave it uncovered at 400°F for 30 minutes, then broil for 2–3 minutes, allowing the cheese to bubble and brown as desired.

This stuffed shell dish goes great with a fresh green salad, garlic bread, or roasted vegetables for a complete meal. In the summer, it’s a smart way to use up garden zucchini and bring something hearty to the table without making a second main dish. Once fall arrives, it becomes the kind of comfort food you’ll want to serve for Sunday dinner, family gatherings, or even as a vegetarian option at Thanksgiving. It also makes a reliable contribution to potlucks or church suppers since it travels well right in the baking dish and reheats nicely.

Leftovers can be stored in the fridge for 3–4 days. Reheat covered with foil at 325°F until warmed through. I don’t recommend freezing this recipe — the zucchini releases extra liquid after thawing, and the pasta shells lose their texture as a result.

Looking for a hearty, veggie-forward dinner that still feels like comfort food? These zucchini stuffed shells with cottage cheese are the answer — simple to make, family-friendly, and always a hit at the table.