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This butternut squash stuffed shells is a creamy and comforting meal. Delicious fall flavors of sage and butternut squash mixed with ricotta cheese are stuffed into pasta shells and covered in a homemade béchamel sauce.

A white baking dish filled with creamy butternut squash stuffed shells, topped with sage leaves.
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Baked till warm and bubbling, these stuffed shells pair wonderfully with a light butter lettuce salad or cast iron roast chicken.

Baked Butternut Squash Stuffed Shells

This is one recipe I love for the fall because it’s really easy to prep, and the whole family will love it. Plus it has sneaky vegetables in it! Instead of your typical baked stuffed shells with marinara, the béchamel is a creamy sauce that pairs well with the ricotta and squash.

You’ll love these squash stuffed shells because:

  • Great for meal prep – I love this recipe to gift to friends or make ahead. All you have to do is prep till you’re ready to bake, then cover and place in the fridge.
  • Fall flavors – The butternut squash and sage pair well with the light, creamy sauce.
  • Easy – This recipe uses canned butternut squash for ease, although you could roast your own if desired (and it would be extra delicious).

This recipe is gluten free friendly if you can find the shells, and migraine diet friendly.

Ingredients

Ingredients for butternut squash stuffed shells on a white marble background.

Here are a few ingredients you will need for these butternut squash stuffed shells. The full list can be found in the recipe card below.

  • Canned butternut squash – I use canned because it’s so easy, but you could substitute fresh, if desired, or use pumpkin instead.
  • Jumbo pasta shells – Large semolina shells are best for stuffing. DeCecco and Barilla shells are two popular brands that will work. Can also use gluten free, but these are harder to find.
  • Ricotta cheese – I recommend a whole milk ricotta that has no carrageenan for the best taste and texture. Liuzzi, Calabro, and BelGiosio are my favorites. These are not grainy and super creamy.
  • Broth – I like to use Trader Joe’s Hearty Vegetable broth for store-bought, or homemade rotisserie chicken broth.
  • Sage leaves – I recommend using fresh for best results, but dried can be used in a pinch. You will need to decrease the amount.

Substitutions

  • Butternut squash – Can be substituted with pumpkin. Make sure you get plain pumpkin puree and not pumpkin pie flavored. Could also be subbed with sweet potato.
  • Goat cheese – Can be substituted with cream cheese, but the flavor will not be as strong.
  • Gluten free – Substitute 1:1 gluten free flour or arrowroot powder for the sauce base and gluten free jumbo shells or noodles.
  • Dairy free – I have not tried this, but would recommend using more butternut squash to substitute the ricotta cheese, then using oat milk for the sauce.

How to Make

Process photos of making the butternut squash stuffing and starting the bechamel sauce.

Step 1: Prep the ingredients

Preheat the oven to 350 degrees Fahrenheit. Cook the pasta according to package directions, then drain and cool. Separate the pasta shells so it doesn’t stick together as it cools. Grease a 9×13 inch pan with a little bit of olive oil.

Step 2: Combine the butternut squash filling

In a large bowl, combine the butternut squash with ricotta, sage, chopped kale or spinach, salt, pepper, and a pinch of nutmeg. Taste and adjust any seasonings. 

Step 3: Stuff the shells

Fill each pasta shell with the butternut/ricotta mixture and set inside the 9×13 inch pan.

Process photos of making the creamy bechamel and pouring it on top of the stuffed shells.

Step 4: Make the béchamel

In a large saucepan, melt the butter over medium-low heat. Stir in the flour till smooth and cook until lightly browned and bubbly. Add the milk and broth in parts, whisking after each addition until smooth. Initially it will be clumpy, but don’t worry, just keep whisking till it smooths out – this is why it’s helpful to do in smaller parts.

Bring the sauce to a simmer, stirring until thickened, about 6-8 minutes. Turn off the heat and stir in goat cheese until smooth. Add any salt and pepper as needed.

Step 5: Bake

Pour the béchamel sauce over the stuffed shells and bake in the oven at 350 degrees Fahrenheit for 25 minutes or until lightly browned and bubbly.

Jumbo shells stuffed with ricotta and butternut squash, topped with a bechamel inside a baking dish next to a striped towel.

Recipe Tips

There are two top tips I have for this recipe. The first is to keep the warm pasta water around in case you forget to separate the shells. If they’re stuck together after cooling/draining, you can just submerge them quickly in the warm water and they should separate easily.

The second is to buy really good quality ricotta cheese. This will make the filling smooth and creamy instead of grainy.

Make Ahead and Storage

Meal prep – To prep ahead, you can make recipe right up till you bake. Before baking, cover the 9×13 dish and place in the fridge. Then bake when ready.

Refrigerator – After baking, allow the stuffed shells to cool completely and then cover them and store in the fridge for up to 3 days. Reheat, covered with foil, at 350 degrees Fahrenheit for about 15 minutes, or until warmed through.

Freezer – This meal freezes very well! You can prep in a freezable baking dish and store for up to 6 months. To cook, allow it to defrost overnight in the fridge before baking.

A wood spoon holding a creamy stuffed shell.

Serving Suggestions

I love these butternut squash stuffed shells on their own, but if you’d like to serve them with either a protein or a side dish, here are my favorite suggestions.

This would also be great served with simple green beans. I have a roasted green bean recipe in The Mediterranean Migraine Diet book.

Frequently Asked Questions

Can I use another type of pasta instead of jumbo shells?

You could do this as a butternut squash lasagna, similar to my lazy lasagna recipe. Just layer the filling with the pasta with the sauce on top.

Could I add chicken?

For a protein, I would definitely choose chicken as the best tasting for these flavors. Would recommend a shredded rotisserie chicken or serving with a recipe like this cast iron roast chicken.

What could I substitute for ricotta cheese?

If you normally hate ricotta cheese, I highly recommend trying one of the brands mentioned above. Full fat ricotta without any additives or thickeners like carrageenan can be smooth and creamy!

What to do with leftover ricotta cheese?

If you have any leftover ricotta cheese, try this whipped ricotta, baked ricotta chicken, or ricotta stuffed chicken.

Pasta Recipes

These butternut squash stuffed shells are one of my favorite vegetarian fall recipes. If you’re craving more comforting flavors, check out these recipes. 

Love this recipe? Please leave a 5-star 🌟🌟🌟🌟🌟 review in the recipe card! Don’t forget to tag me @thedizzycook on Facebook and Instagram, and follow along on Pinterest for more great recipes!

A white baking dish with butternut squash and ricotta stuffed jumbo shells.
5 from 10 votes
Servings: 4 people

Butternut Squash Stuffed Shells

These butternut squash stuffed shells have the perfect fall flavors of sage and butternut mixed with a creamy cheese sauce. This vegetarian dish is cozy and comforting, plus a great way to sneak in some extra vegetables!
Prep: 20 minutes
Cook: 25 minutes
Total: 45 minutes
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Ingredients 

  • 12 oz jumbo pasta shells
  • 15 oz can of butternut squash*
  • 1.5 cups ricotta cheese
  • 2 tablespoons fresh sage leaves, minced
  • 1 cup fresh kale or spinach, chopped
  • 1 teaspoon kosher salt
  • 1/4 teaspoon black pepper
  • pinch of nutmeg

Creamy Bechamel Sauce

  • 2 tablespoons butter
  • 2 tablespoons all purpose flour
  • 3/4 cup milk
  • 3/4 cup broth (chicken or vegetable)
  • 3 ounces chèvre goat cheese or cream cheese

Instructions 

  • Preheat oven to 350 degrees F. Cook the pasta according to package directions for "al dente", usually on the lower end of the cooking time. The pasta should be softened, but still firm (not mushy). Drain and set shells aside on a towel.
    Unbaked butternut squash stuffed shells in a white baking dish
  • Grease a 9×13 inch pan with a little olive oil or extra butter. In a large bowl, combine the butternut squash with ricotta, sage, chopped kale or spinach, salt, pepper, and a pinch of nutmeg. Taste and adjust any seasonings. Fill each pasta shell with the butternut/ricotta mixture and set inside the 9×13 inch pan.
  • In a large saucepan, melt the butter over medium-low heat. Stir in the flour till smooth and cook until lightly browned and bubbly. Add the milk and broth in parts, whisking after each addition until smooth.
  • Initially it will be clumpy, but don't worry, just keep whisking till it smooths out – this is why it's helpful to do in smaller parts. Bring the sauce to a simmer (small bubbles), stirring until thickened, about 6-8 minutes. Turn off the heat and stir in goat cheese until smooth. Add any salt and pepper as needed.
  • Pour the sauce over and around the shells. Bake at 350 degrees F for 25 minutes until lightly browned and bubbly on the top. Serve warm!

Notes

  • Butternut squash can be substituted with plain canned pumpkin or sweet potato. 
  • The serving size calculated for this is for 4 people, which is a very generous serving that would be a full meal. This could stretch to serve 6 people easily. 
  • For migraine-friendly, check the ricotta cheese for additives (use brands suggested in post) and also use homemade vegetable broth from my cookbook or this chicken stock.
  • I find canned butternut squash the fastest/easiest, but see the post for suggestions for cooking fresh in an instant pot. 
 

Nutrition

Calories: 683kcal, Carbohydrates: 86g, Protein: 29g, Fat: 25g, Saturated Fat: 11g, Cholesterol: 76mg, Sodium: 623mg, Potassium: 803mg, Fiber: 5g, Sugar: 8g, Vitamin C: 42mg, Calcium: 366mg, Iron: 3mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Like this? Leave a comment below!

Alicia

Alicia is a vestibular migraine advocate and the bestselling author of The Dizzy Cook: Managing Migraine with More Than 90 Comforting Recipes and Lifestyle Tips. Her articles and recipes have been featured by Healthline, Parade, mindbodygreen, Today, Good Morning Texas, the Vestibular Disorders Association, and the American Migraine Foundation. Read More

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5 from 10 votes (2 ratings without comment)

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Recipe Rating




15 Comments

  1. Andrie says:

    5 stars
    I love this recipe. It’s easy and tastes delicious. Even my kids loved it so definitely I will make it again.

  2. Kyndall says:

    5 stars
    This recipe is a keeper! My husband isn’t always thrilled about my migraine diet limitations (but he gives his best effort and I love him for that). This one is staying in our rotation though it was soooo delicious and comforting.

  3. barbara giuliano says:

    I would like to make this for xmas..Can I make it a day before but stuff the shells that morning? then bake of course.

    1. Alicia says:

      Yes, that’s a great idea!

  4. mangomama says:

    5 stars
    This was delicious! I tweaked it just a bit ( since I couldn’t find canned butternut squash), using roasted butternut squash (about 3 cups total)– coarsely mashed about 2 cups before mixing it with other filling ingredients then used about 1 cup of the roasted squash to garnish the edges of the casserole dish. Thanks for the recipe!

  5. Kerry says:

    Can I use pumpkin instead? I will be baking them this weekend!

    1. Alicia says:

      Yes pumpkin works!