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Kabocha Squash Mac and Cheese

In a previous post, ZEST Nutrition described what is kabocha squash and how to serve it with a simple sweet sauce. In general, kabocha squash is green on the outside and has orange flesh on the inside. It's harvested in the fall in the US.

It’s starchier than butternut squash and pumpkin, but sweeter like sweet potato. Because of its smaller size, several cultures have been using kabocha in place of pumpkin to reduce waste while adding nutrition, flavor, and texture to their meals.

Kabocha squash is extremely versatile. It can be roasted and eaten plain. It can be added to salad. Kabocha can be sliced into half moon shapes and served with a sweet sauce. Here, though, we add kabocha squash to mac and cheese.

kabocha squash cut in half
Kabocha Squash

Why Add Kabocha Squash to Mac and Cheese?

Kabocha squash is rich in vitamin A. Boasting 130% of the vitamin A RDA, it helps improve night vision and prevent age-related macular degeneration. Vitamin A is also important for bone health and preventing cancer.

Kabocha also contains vitamin C (12% RDA) as well as potassium. A serving has only 8g of carbohydrates, which is great for people with diabetes who are counting carbs. It is also low in calories- only 35 calories per 100g.

In recent years, pumpkin mac and cheese has become popular. However, using actual pumpkin from a baking pumpkin requires more work than using a kabocha squash. (Using canned pumpkin, which may actually be pumpkin or another squash, is the easiest option, though!)

Kabocha is small enough to use for four-six servings. It requires cutting it in half, scooping out the seeds with a spoon from each half, and baking it for about a half hour to 45 minutes. From there, the squash can be mashed or pureed and added to your basic mac and cheese.

How to Cut Kabocha Squash

The easiest way to cut kabocha squash is by following these steps:

  1. Rinse the kabocha squash and dry it with a paper towel.

  2. Soften the rind by placing it in the microwave for 4 minutes. (If you don’t have a large enough microwave, you can cut it in half and microwave each half for 2 minutes, or according to Just One Cookbook, you can wrap it in foil and put it in an oven at 400° for 15 minutes.)

  3. Next, slice off a sliver of one side so you have a flat surface to lay the squash on.

  4. With the squash laying safely on its flat side, cut off the stem by slicing into the squash about a half inch under the stem.

  5. Cut the squash in half.

  6. Scoop out the seeds with a large soup spoon. (This is simple, unlike trying to get the seeds out of a pumpkin.)

  7. If you want to speed up baking time, slice into wedges. If baking time is not an issue, leave the squash in halves so it's easier to scoop out of the rind.

Kabocha Squash Mac and Cheese Recipe

pot of kabocha squash mac and cheese


  • 1 Tbsp oil

  • 1 cup mashed or pureed kabocha squash

  • 2 Tbsp butter or plant-based spread

  • 2 Tbsp gluten-free flour

  • 2 cups 2% milk, soymilk, hemp, or rice milk

  • 4 oz cheddar cheese, shredded

  • 6 oz gruyere cheese, shredded

  • 1/2 teaspoon salt

  • pinch nutmeg

  • pinch cinnamon

  • 1 -16 oz. box of gluten-free pasta (elbows, shells, or fusilli)


  1. Using the instructions above to cut the kabocha squash in half, place on a sheet pan, drizzle with oil, and bake at 400°F for 35 minutes. (If cut into wedges, bake about 25 minutes and then remove the rinds once cool.)

  2. When the squash is done baking, remove it from the oven and let it cool on a plate in the fridge.

  3. While the kabocha squash cools, make roux by adding butter (or plant-based spread) and flour to a large soup pot over medium heat. Whisk briskly until combined.

  4. Slowly start adding milk about one quarter cup at a time. Whisk after each addition and only add the next quarter cup when the milk has been absorbed by the roux. This process will take approximately 30 minutes.

  5. Once all of the milk has been added and a thick sauce has formed, turn the heat off, add the cheese, and stir.

  6. Now scoop 1 cup (or more if preferred) of squash into a blender and roughly puree. You can add a little water if necessary. (If you don’t have a blender, put the squash in a large bowl and mash with a potato masher.)

  7. Add the squash, salt, nutmeg, and cinnamon to the cheese sauce and stir well.

  8. Boil the pasta and cook according to package instructions. In the meantime, return the cheese sauce to a low heat and stir occasionally to prevent it from sticking to the bottom of the pot.

  9. Drain the cooked pasta and pour it into a baking pan or whatever it will be served from. Pour the cheese sauce over it.

  10. Garnish with a sprinkle of your favorite herb or spice and serve.

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