Butternut squash manicotti

This tasty butternut squash manicotti recipe has it all – sweet butternut squash, creamy Alfredo sauce, and savory rosemary and nutmeg. This is a great recipe to turn to when you are looking to impress. Whether you are cooking for a room full of friends or you just want to treat yourself to a special meal, this one is a true crowd pleaser. 

This recipe for butternut squash manicotti is made with gluten free manicotti noodles, but if you do not have a gluten intolerance you could also make it with regular manicotti noodles. In addition to being gluten free, this recipe is also vegetarian, nut free, and egg free.

What is manicotti?

What is manicotti? If you do not eat a lot of Italian food you might not be familiar with manicotti. Heck, even if you do eat a lot of Italian food you still might not be familiar with manicotti. Manicotti is a long tube shaped pasta that is generally around 4-6 inches long. Manicotti noodles have a large opening that is about 1 inch in diameter so you can stuff the noodles with your favorite filling. I love manning manicotti because I get to use all of my favorite ravioli stuffings without actually making any noodles myself.

Where to get gluten free manicotti

Where can you get gluten free manicotti? There are lots of brands that make gluten free penne, spaghetti, and elbow noodles out there. Gluten free manicotti, on the other hand, is not so easy to find. I generally use Jovial Foods brand manicotti noodles when I am making gluten free manicotti. These noodles are free of the most common allergens and they hold up well after being cooked. 

How to cook manicotti

How do you cook manicotti noodles? Manicotti noodles are cooked in 2 stages. First they are boiled for 3-4 minutes so that they are pliable but still firm. After that they are filled with a filling and cooked again until they become soft and tender. Manicotti noodles are similar to lasagna noodles that need to be pre-cooked. 

In many manicotti recipes, the manicotti noodles are put in the oven and baked at a low temperature for 30-40 minutes after they are filled. In this recipe I cook my manicotti on the stovetop. There are two reasons for this. First, the manicotti noodles cook faster on the stovetop. Second, the Alfredo sauce I am using is likely to curdle in the oven. When you cook the manicotti noodles on the stovetop it is much easier to wait to add the parmesan cheese until the very end to prevent curdling. 

What to do if a manicotti noodle breaks

What do you do if a manicotti noodle breaks? Sometimes manicotti noodles break before they even come out of the box from being manhandled during transportation. Other times manicotti noodles split down the middle during the first round of cooking. You should handle your noodles differently depending on whether they have broken into multiple shorter tubes or split in half lengthwise so that they start to unravel into a large sheet. 

If you manicotti noodles break into multiple shorter tubes it is more difficult to work with them. If the noodles break in half it is one thing, but if they break into multiple smaller pieces then they are going to be hard to work with because the stuffing is going to fall out. In this case, I usually toss the noodles or repurpose them in another noodle dish like mac and cheese where the noodles do not need to hold a filling. 

If a manicotti noodle splits down the middle lengthwise it is easier to work with it. You can still fill the length of the noodle up with stuffing but laying the noodle flat on a table and piping filling into it. The main difference for working with split manicotti noodles is that you should not flip the noodles over at any time after filing it. Always keep the seam along which the noodle has split on the top so the filling does not fall out. 

When you cook the split noodle for the second time in the oven or on the stove you should sandwich the split noodle tightly between two intact noodles. This way the intact noodles will help hold the split noodle in shape. You can make sure that the top of the split noodle gets cooked by spooning warm sauce over the top of it every minute or two. 

How to cook butternut squash

If you have cooked butternut squash before, you know the drill. If you have not cooked butternut squash before I am here to tell you that it is surprisingly easy! We go through all of the steps you need to go through in this recipe but if you want a more comprehensive guide with step-by-step pictures you should check out our comprehensive tutorial on how to cook butternut squash.

Butternut squash manicotti

These delicious butternut squash manicotti are topped with a creamy alfredo sauce.
Prep Time25 minutes
Cook Time20 minutes
Inactive time (while squash roasts)1 hour
Total Time1 hour 45 minutes
Course: Main Course
Cuisine: Italian
Diet: Gluten Free, Vegetarian
Keyword: egg free, gluten free, nut free, vegetarian
Servings: 10 manicotti


Roasted butternut squash & garlic

  • 1 butternut squash
  • 3 cloves garlic
  • 1 tsp olive oil
  • 1/8 tsp salt

Butternut squash filling

  • 2 cups roasted butternut squash (from previous step)
  • 3 cloves roasted garlic (from previous step)
  • 1 cup ricotta cheese
  • 1/2 cup cup frozen spinach
  • 2 tsp dried rosemary
  • 1/4 tsp salt

Nutmeg alfredo sauce

  • 2 cups cream
  • 1 1/2 cup parmesan cheese (vegetarian parmesan style cheese)
  • 1 tbsp cream cheese
  • 2 tsp gluten free all purpose flour
  • 1 tbsp butter
  • 1 tsp nutmeg
  • 4 sprigs fresh thyme (use only the leaves)


  • 10 gluten free manicotti noodles


Roasted butternut squash & garlic

  • Preheat your oven to 350 degrees.
  • Cut the butternut squash in half lengthwise and use a metal spoon to scrape out the seeds and stringy bits in the bulb. Brush the butternut squash with olive oil and top it with salt. Put the butternut squash on a baking sheet lined with tin foil with the flat side down.
  • Peel the garlic and brush it with olive oil then put the garlic under butternut squash in the dome where the seeds used to be. This will prevent the garlic from overcooking and drying out
  • Bake the butternut squash and garlic in the oven at 350 degrees for 1 hour.

Butternut squash filling

  • Once the butternut squash is done cooking you can start to assemble the butternut squash filling. But first, start boiling a medium sized pot of water over high heat. We will use this in the next section to pre-cook the manicotti.
  • Mash the roasted butternut squash and the roasted garlic then mix them with all of the other ingredients for the butternut squash filling.
  • You will need to pipe the butternut squash filling into the center of the manicotti. If you do not have a proper piping bag you can scoop the filling into a plastic sandwich bag and cut 1 cm off of the corner of the bag to create an opening that is 1-2 cm wide.

Assembling the butternut squash manicotti

  • Boil the manicotti noodles to pre-cook them according to the instructions on the package. Generally the manicotti will need to be boiled for around 4-5 minutes. You want the manicotti to be relatively firm when they are done so that you can stuff them without any difficulty.
  • When the manicotti are done cooking you should pipe the butternut squash filling into the center of the manicotti. The entire noodle should be filled with the butternut squash filling.
  • Make a roux for the nutmeg alfredo sauce by mixing the butter and flour in a large flat pan over medium heat. Cook the roux for 1-2 minutes then slowly incorporate the cream into the roux.
  • Add the manicotti to the pan so that all of the manicotti are touching the bottom of the pan. Cook the manicotti over medium heat for 10-15 minutes or until the noodles are tender. Flip the noodles over every few minutes so that they cook evenly.
  • When the manicotti are done cooking, reduce the heat to low and mix in the rest of the ingredients for the Alfredo sauce. You may need to remove the manicotti from the pan to mix the alfredo sauce depending on how large your pan is. You should add the cream cheese, nutmeg, and thyme leaves first then add the parmesan cheese after the cream cheese has dissolved into the cream.

Substitutions for butternut squash manicotti

  • If you do not have fresh thyme you can use 1 1/2 tsp of dried thyme.
  • The cream cheese in the Alfredo sauce is not absolutely essential here. I just use it because it contains stabilizers that help prevent the alfredo sauce from curdling. 

Other recipes you might like

halved butternut squash

If you have any questions about how to roast a butternut squash or if you are looking for other recipes that contain butternut squash you should check out our comprehensive guide on butternut squash.

Butternut squash ravioli

If you have any butternut squash manicotti filling leftover you could always repurpose to make these gluten free butternut squash ravioli. I like to make a double batch of butternut squash filling when I make manicotti and make some ravioli the next day. 

Butternut squash alfredo pasta

If you like the idea of butternut squash and Alfredo sauce but you cannot find manicotti noodles, you should check out our recipe for Alfredo pasta with butternut squash.

gluten free butternut squash ricotta gnocchi

If you want to try your hand at making some homemade pasta with butternut squash then you should check out our recipe for butternut squash gnocchi. These butternut squash ricotta gnocchi are even easier to make than potato gnocchi.

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